Jmenzago Week 6
Purpose
This research assignment seeks to find a location on the env gene of HIV-1 that differentiates rapid progressors from nonprogressors, with the hopes of locating a region that can be targeted for efficient treatment of HIV. If mutations occur frequently within a specific location on the env gene of rapid progressor strains and not as frequently in nonprogressors, then that region can be targeted to develop more efficient treatment methods.
Methods/Results
Subject Selection
- Five subjects selected for analysis based on dS/dN values
- Only rapid and nonprogressors chosen
- Subjects with the two highest and two lowest non-zero dS/dN values selected
- Subject 3 selected because dS/dN value was 1.0
- If dS/dN theory is correct, the perfect ratio would indicate that the strain is a moderate progressor, but Subject 3 was classified as a rapid progressor
- Total of 78 clones analyzed
- 34 from first visit
- 44 from last visit
Subject | Progression | Median dS/dN |
---|---|---|
1 | Rapid | 0.3 |
2 | Non | 1.8 |
3 | Rapid | 1.0 |
10 | Rapid | 0.2 |
13 | Non | 3.5 |
Comparison of Sequences
- Align all sequences from the first visit for each subject and all sequences for the last visit for each subject for the nonprogressors
- Align on www.phylogeny.fr
- "One Click" under "Phylogeny Analysis"
- Upload FASTA sequences for subjects in Table 1 from first visit and submit.
- Export alignment as clustal format
- Upload FASTA sequences for subjects in Table 1 from last visit and submit.
- Export alignment as clustal format
- Align on www.phylogeny.fr
- Repeat for rapid progressors
- Aligned sequences for first visits of nonprogressors:
S13V1-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-3 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S2V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTGAAATCATAATAGTACAGCTG S2V1-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG *** ************* *********** ********* ********************
S13V1-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V1-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S2V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT ** ***************************** ************** ******* **
S13V1-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-3 ATAGGACCAGGGAGAGCATTCTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-4 ATGGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S2V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAAGAGATATAAGACAAGCA S2V1-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA ** ******** ******** *** ** ** *** ****** *****************
S13V1-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S2V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG *********** **** **** ***** ***** ***** **** *** * ******
S13V1-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S2V1-5 AGAGAACACTTTGGAAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-4 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-1 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V1-3 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-2 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA ******** *** * *** ************* *** ** ***
- Aligned sequences for last visit of nonprogressors:
S13V5-3 GAGATAGTAATTAGATTTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-6 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S13V5-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-5 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S2V4-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCCG S2V4-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-8 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTA S2V4-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-9 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG *** ************ *********** ************* **************
S13V5-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-6 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-5 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S2V4-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-4 AATGAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-7 AATGAATCTGTAGAAATTAATTGTACAAAACCCAACAACAATACAAGAAAAAGTATACAT S2V4-6 AATGAGTCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAGAAAGTATACAT S2V4-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT ** ** ***************** **** **** ************* ******* **
S13V5-3 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-6 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-4 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-5 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S2V4-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V4-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V4-8 ATAAGACCAGGTAGAGCATTTTATACAACAAGAGACATAATAAGAGAGATAAGACAAGCA S2V4-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-7 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V4-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-9 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA *** ******* ************ ** ** ** ****** **** ************
S13V5-3 TATTGTAACATCAGTAAAGCGAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-6 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V5-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V5-2 TATTGTAACATCAGTAAAGCAAAATGGGACAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-5 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S2V4-3 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-5 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-8 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAATTA S2V4-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAATTA S2V4-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-7 CATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-9 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA ********** **** *** ***** * ********* **** *** * *******
S13V5-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-6 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-5 AGAGAACAATTTAAGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S2V4-3 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAGCCACTCCTCA S2V4-5 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V4-8 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-1 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-2 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-4 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-7 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-9 AGAAAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA *** **** *** **** ************* ** ** ***
- Calculate the S values per bins of 15 nucleotides (5 codons) for each aligned sequence
- S values summarized in Table 2 and Table 3
- The aligned sequences from the last visit have one more codon than those from the first visit (288 nucleotides vs. 285 nucleotides), so it was not counted
- the extra codon had no invariants, should not impact the outcome of this experiment
Window | First Visit | Last Visit |
---|---|---|
1 | 1 | 1 |
2 | 2 | 3 |
3 | 1 | 1 |
4 | 0 | 2 |
5 | 1 | 2 |
6 | 0 | 2 |
7 | 3 | 2 |
8 | 2 | 3 |
9 | 2 | 2 |
10 | 3 | 2 |
11 | 4 | 5 |
12 | 0 | 1 |
13 | 1 | 2 |
14 | 3 | 5 |
15 | 3 | 2 |
16 | 5 | 4 |
17 | 3 | 4 |
18 | 3 | 3 |
19 | 3 | 4 |
Window | First Visit | Last Visit |
---|---|---|
1 | 2 | 6 |
2 | 4 | 7 |
3 | 2 | 2 |
4 | 2 | 2 |
5 | 5 | 5 |
6 | 4 | 5 |
7 | 2 | 4 |
8 | 5 | 9 |
9 | 6 | 6 |
10 | 4 | 6 |
11 | 5 | 10 |
12 | 4 | 6 |
13 | 2 | 4 |
14 | 4 | 7 |
15 | 7 | 4 |
16 | 5 | 10 |
17 | 5 | 5 |
18 | 3 | 3 |
19 | 2 | 5 |
- Generate a graph plotting the S value vs. the bin number for the first and last visit for both the nonprogressors and rapid progressors
- Graphs were generated using Excel
- Graph for S values of nonprogressors
- Graph for S values of rapid progressors
- No window showed clear favor for mutations
- It is possible that window 11 is a favored target for mutation
- nonprogressors only had a difference of 1 invariant between visits
- rapid progressors had a difference of 5 invariants between sequences
Generation of Phylogenetic Tree
- Generate a phylogenetic tree for all the clones from the first and last visits for the subjects chosen for the study
- Tree will show if rapid progressors showed similar mutations, suggesting that certain mutations code for rapid progression
- Generate tree on www.phylogeny.fr
- "One Click" under "Phylogeny Analysis"
- Upload FASTA files of all sequences for the first and last visits of subjects chosen for the study and submit, tree will generate
- Phylogenetic tree for all clones of HIV-1 from the first and last visits for the subjects chosen for this study:
- Aligned sequences for first visits from subjects used for tree:
S3V1-3 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V1-4 GATGTAGTAATCAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V1-1 GATGTAGTAATTAGATCCGCCAATTTCTCGGACAATGCTAAAACCATACTAGTACAGCTG S3V1-2 GATGTAGTAATTAGATCCGCCAATTTCTCGGACAATGCTAAAACCATACTAGTACAGCTG S13V1-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-3 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S10V1-5 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-2 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-3 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-4 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAATACAGCTG S10V1-6 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-7 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-1 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S1V1-13 GAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S1V1-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-10 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTGAAATCATAATAGTACAGCTG S2V1-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-7 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-8 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-9 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-12 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-11 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG ** ******* ***** * ****** * ******** *** **** ** ********
S3V1-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V1-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V1-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V1-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S13V1-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V1-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S10V1-5 AATAAATCTGTAGAAATTAATCGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-2 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-3 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-4 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-6 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-7 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-1 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S1V1-13 AATACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-10 GATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-6 AATGAATCTGTAGAAATTAACTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-12 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-11 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT * * ****** *** ** * ******** ************** *** ** *
S3V1-3 CTAGGACCAGGCAAAGTATACTACACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-4 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-1 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-2 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S13V1-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-3 ATAGGACCAGGGAGAGCATTCTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-4 ATGGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S10V1-5 ATGGGGCCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S10V1-2 ATGGGACCAGGGAGAGCATTATATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S10V1-3 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAACAGGAGATATAAGGCAAGCA S10V1-4 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S10V1-6 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGGAATAATAGGAGATATAAGGCAAGCA S10V1-7 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S10V1-1 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S1V1-13 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACCAGCA S1V1-2 ATAAGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAAGAGATATAAGACAAGCA S1V1-10 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAGGCA S1V1-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAAGAGATATAAGACAAGCA S2V1-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-7 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAGGCA S1V1-8 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAGGCA S1V1-9 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAGGCA S1V1-12 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAGGCA S1V1-11 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA * * ***** * ** ** ** ** ** ** **** * ********** ***
S3V1-3 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-4 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-1 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-2 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S13V1-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S10V1-5 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-2 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-3 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-4 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-6 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-7 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-1 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S1V1-13 TATTGTAACATTAGTAGAGCAGAATGGGATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACACCTTAAAACACATAGTTATAAAATTA S1V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAACAAATTA S1V1-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-10 TATTGTAACATTAGTAGAGCAGAATGGGATAACACTTTAAAACAGATAGGTATAAAATTA S1V1-1 TATTGTAACATTAGTAGAGCAGAATGGGATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAGACAGATAGTTATAAAATTA S2V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S1V1-7 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-8 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-9 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-12 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-11 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAATCAGATAGTTATAAAATTA S1V1-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA ******** * **** * ** * *** ** ** * *** *** * *****
S3V1-3 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V1-4 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V1-1 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V1-2 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S13V1-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S10V1-5 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-2 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-3 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-4 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-6 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-7 GGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-1 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S1V1-13 AGAGAACACTTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-4 AGAGAACACTTTGGCAACAAAACAATAGTCTTTAATCACTCTTCA S1V1-5 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-2 AGAGAACACTTTAGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-10 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-1 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCTTCA S1V1-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V1-5 AGAGAACACTTTGGAAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-4 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-1 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V1-3 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-2 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S1V1-7 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-8 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-9 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-12 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-11 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-3 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA ******* *** ** ****** ***** *** ** ***
- Aligned sequences for last visits from subjects used for tree:
S3V6-2 GATGTAGTAATCAGATCTGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-4 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-5 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-3 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-6 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-1 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S13V5-3 GAGATAGTAATTAGATTTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-6 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S13V5-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-5 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S10V6-2 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-3 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V6-7 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-6 GAGGTAGCAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-8 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-9 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-10 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-1 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-4 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S10V6-5 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACATCTG S1V5-2 GAGGTAGTAGTTAGATCCGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTG S1V5-5 GAGGTAGTAGTTAGATCCGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTG S1V5-1 GAGGTAGTAGTTAGATCCGAAAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S1V5-12 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTG S1V5-13 GAGGTAGTAGTTAGGTCTGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTG S1V5-8 GAGGTAGTAGTTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACATCTG S1V5-10 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACATCTG S2V4-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCCG S2V4-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-8 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTA S2V4-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-9 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V5-11 GAGGTAGTAGTTAGATCCGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTG S1V5-3 GAGGTAGTAATTAGATCCGAAAATATCGCGAACAATGCTAAAATCATAATAGTACAGCTG S1V5-4 GAGGTAGTAATTAGATCTGAAAATATCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V5-6 GAGGTAGTAATTAGATCTGAAAATATCATGAACAATGCTAAAATCATAATAGTACAGCTG S1V5-9 GAGGTAGTAATTAGATCTGAAAATATCATGAACAATGCTAAAATCATAATAGTACAGCTG S1V5-7 GAGGTAGTAATTAGATCTGAAAATATCATGAACAATGCTAAAATCATAATAGTACAGCTG ** *** * * ** * * *** ** ************ **** ******* *
S3V6-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S3V6-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S3V6-5 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S3V6-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S3V6-6 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S3V6-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTA--- S13V5-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S13V5-6 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S13V5-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S13V5-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S13V5-5 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S13V5-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATA--- S10V6-2 AATAAATCTGTAGAAATTAATTGCACAAGACCCAATAACAATACAAGAAGAAGTATA--- S10V6-3 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-7 AATAAAGCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-6 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-8 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-9 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-10 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-1 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATA--- S10V6-4 AATGAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATAAAAGAAAAAGAATC--- S10V6-5 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATAAAAGAAAAAGAATA--- S1V5-2 AATAAATCTGTAAACATTAGTTGTATAAGACCCAACAACAATACAAGAAGAAGTATA--- S1V5-5 AATAAATCTGTAAACATTAGTTGTATGAGACCCAACAACAATACAAGAAGAAGTATA--- S1V5-1 AATAAATCTGTAAACATTAGTTGTATGAGACCCAACAACAATACAAGAAAAAGTATA--- S1V5-12 AATAAACCTGTAAACATTAGTTGTATGAGACCCAACAACAATACAAG---AAGTATA--- S1V5-13 AATAAATCTGTAAACATTAGTTGTATGAGACCCAACAACAATACAAGAAGAAGTATA--- S1V5-8 AATGAATCTGTAGGAATTAATTGTACAAGACCCAACAACAATATAAAAAAAAGAATAATA S1V5-10 AATGAATCTGTAGGAATTAATTGTACAAGACCCAACAACAATATAAAAAAAAGAATAATA S2V4-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-4 AATGAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V4-7 AATGAATCTGTAGAAATTAATTGTACAAAACCCAACAACAATACAAGAAAAAGTATA--- S2V4-6 AATGAGTCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAGAAAGTATA--- S2V4-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S1V5-11 AATAAATCTGTAAACATTAGTTGTATGAGACCCAACAACAATATAAAACAAAGAATAATG S1V5-3 AATGAATCTGTAGCAATTAATTGTACAAGACCCAACAACAATATAAAACAAAGAATAATA S1V5-4 AATGAATCTGTAGCAATTAGTTGTACAAGACCCAACAACAATATAAAACAAAGAATAATG S1V5-6 AATGAATCTGTAGCAATTAATTGTACAAGACCCAACAACAATATAAAACAAAGAATAATG S1V5-9 AATGAATCTGTAGCAATTAATTGTACAAGACCCAACAACAATATAAAACAAAGAATAATG S1V5-7 AATGAATCTGTAGCAATTAATTGTACAAGACCCAACAACAATATAAAACAAAGAATAATG ** * ***** ** * *** * * **** ******* ** *** *
S3V6-2 ACTCTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAA S3V6-4 ACTCTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAA S3V6-5 ACTCTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAA S3V6-3 ACTCTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAA S3V6-6 ACTCTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAA S3V6-1 ACTCTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAA S13V5-3 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V5-6 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V5-4 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V5-2 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V5-5 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V5-1 AATATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S10V6-2 AATATGGGACCAGGGAGAGCATTCTATACAACAGGAGACATAATAGGAGATATAAGGCAA S10V6-3 AATATGGGACCAGGGAGAGCATTGTATACAACAGGAGACATAATAGGAGATATAAGGCAA S10V6-7 AATATGGGACCAGGGAGAGCATTTTATGCAACAGGAGACATAATAGGAGATATAAGGCAA S10V6-6 AATATGGGACCAGGGAGAGCATTTTATGCAACAGGAGACATAATAGGAGATATAAGGCAA S10V6-8 AATATGGGACCAGGGAGAGTATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAA S10V6-9 AATATGGGACCAGGGAGAGTATTTTATGCAACAGGAGAAATAATAGGAGATATAAGGCAA S10V6-10 AATATGGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGGCAA S10V6-1 AATATGGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGGCAA S10V6-4 AATATGGGACCAGGGAGAGTATTGTATACAACAGGAGAAATAATAGGAGATATAAGGCAA S10V6-5 ACTATGGGACCAGGGAGAGCATTGTATACAACAGGAGAAATAATAGGAGATATAAGGCAA S1V5-2 AATATAGGACCAGGTAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGACCA S1V5-5 AATATAGGACCAGGTAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGACAA S1V5-1 AATATAGGACCAGGTAGAGCATTTTATACAACAGAAGACATAATAGGAGATATAAAACCA S1V5-12 AATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S1V5-13 AATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S1V5-8 CATATAGGACCAGGTAGAGCATTTTATACAA---GAGAC---AAAGGAGATATAAGACAA S1V5-10 CATATAGGACCAGGTAGAGCATTTTATACAA---GAGAC---AAAGGAGATATAAGACAA S2V4-3 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAA S2V4-5 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAA S2V4-8 CATATAAGACCAGGTAGAGCATTTTATACAACAAGAGACATAATAAGAGAGATAAGACAA S2V4-1 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S2V4-2 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S2V4-4 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S2V4-7 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAA S2V4-6 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S2V4-9 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S1V5-11 CATATAGGACCAGGTAGAGCATTTTATACAA---AAGACATAACAGGGGATATAAGACAA S1V5-3 CATATAGGACCAGGTAGACCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S1V5-4 CATATAAGACCAGGTAGAGCATTTTATACAA---AAGACATAACAGAAGATATAAGACAA S1V5-6 CATATAGGACCAGGTAGAGCATTTTATACCA---AAGACATAACAGGGGATATAAGACAA S1V5-9 CATATAGGACCAGGTAGAGCATTTTATACAA---AAGACATAACAGGGGATATAAGACAA S1V5-7 CATATAGGACCAGGTAGAGCATTTTATACAA---AAGACATAACAGGGGATATAAGACAA * * ******* *** ** *** * * * * ** **** *
S3V6-2 GCACATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAGAAAGGATAGCTATAAAA S3V6-4 GCACATTGTAACCTTAGTAGAGCGGATTGGAATAACACTTTAGAAAGGATAGCTATAAAA S3V6-5 GCACATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAGAAAGGATAGCTATAAAA S3V6-3 GCACATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAA S3V6-6 GCACATTGTAACCTTAGTAGAGCAGGTTGGAATAGCACTTTAGAAAGGATAGCTATAAAA S3V6-1 GCACATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAA S13V5-3 GCATATTGTAACATCAGTAAAGCGAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAA S13V5-6 GCATATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAA S13V5-4 GCATATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAA S13V5-2 GCATATTGTAACATCAGTAAAGCAAAATGGGACAACACTTTAGGACAGGTAGCTGCAAAA S13V5-5 GCATATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAA S13V5-1 GCATATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAA S10V6-2 GCACATTGTAACCTTAGTAGAACAGAATGGAATGACACTTTAAAACAGGCTGTCGACAAA S10V6-3 GCACATTGTAACATTAGTAGAACAGAATGGAATGACACTTTAAAACAGGTAGTTGACAAA S10V6-7 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGCTGTTGCCAAA S10V6-6 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAAGTAGTTGACAAA S10V6-8 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAA S10V6-9 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGCCAAA S10V6-10 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAA S10V6-1 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGCCAAA S10V6-4 AGATATTGTAACCTTAGTAGAACAGAATGGAATGACACTTTAAAACAAGTAGTTGACAAA S10V6-5 AGATATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGGTGCTGACAAA S1V5-2 GCACATTGTAACATTAGTAGAGCAGACTGGAATAACACTTTAAAACAAATAGTTATGAAA S1V5-5 GCACATTGTAACATTAGTAGAGCAGACTGGAATAACACTTTAAAACAAATAGTTATGAAA S1V5-1 GCACATTGTAACATTAGTAGAGCAGACTGGAATAACACTTTAAAACAAATAGTTATGAAA S1V5-12 GCACATTGTAACATTAGTGGAACAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-13 GCACATTGTAACATTAGTGGAGCAGCATGGAATAACACTTTAAAAGAGATAGTTATGAAA S1V5-8 GCATATTGTAACATTAGTAGAGCAGACTGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-10 GCATATTGTAACATTAGTAGAGCAGCACGGAATAACACTTTAAAACGGATAGTTAAAAAA S2V4-3 GCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-5 GCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-8 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-1 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAA S2V4-2 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAA S2V4-4 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-7 GCACATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-6 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V4-9 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S1V5-11 GCATATTGTAACATTAGTAGAACAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-3 GCACATTGTAACATTAGTGGAGCAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-4 GCATATTGTAACATTAGTAGAACAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-6 GCATATTGTAACATTAGTAGAACAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-9 GCATATTGTAACATTAGTAGAACAGCATGGAATAACACTTTAAAACAGATAGTTAAAAAA S1V5-7 GCATATTGTAACATTAGTAGAGCAGCATGGGATAACACTTTAAAACGGATAGTTAAAAAA * ******** * *** * * ** * ******* * * ***
S3V6-2 TTAAGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-4 TTATGAGAACAATTTCAGAATAAAACAATAGGCTTTAATCAATCCTCA S3V6-5 TTAAGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-3 TTAAGAGAACAATTTCAGAATAAAACAATAGCCTTTAACCAATCCTCA S3V6-6 TTAAGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-1 TTAAGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S13V5-3 TTAAGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-6 TTAAGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-4 TTAAGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-2 TTAAGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-5 TTAAGAGAACAATTTAAGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-1 TTAAGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S10V6-2 TTAAGAGAACAATTTAGGAACAAAACAATAATCTTTAATCAATCCTCA S10V6-3 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V6-7 TTAAGAGAACAATTTAGGAACAAAACAATAATCTTTACTCAATCCTCA S10V6-6 TTAAGAGAACAATTTAGGAACAAAACAATAATCTTTAATCAATCCTCA S10V6-8 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V6-9 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTACTCAATCCTCA S10V6-10 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTACTCAATCCTCA S10V6-1 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTACTCAATCCTCA S10V6-4 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V6-5 TTAAGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S1V5-2 TTAGGAGAACACTTGGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-5 TTAGGAGAACACTTGGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-1 TTAGGAAAACACTTGAGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-12 TTAGGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-13 TTAGGAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-8 TTAAGAGAACACTTTGTGAATAAAACAATAGTCTTTAACCACTCCTCA S1V5-10 TTAGGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-3 TTAAGAAAACAATTTGAGAATAAAACAATAGTCTTTAGCCACTCCTCA S2V4-5 TTAAGAAAACAATTTGAGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V4-8 TTAAGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-1 TTAAGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-2 TTAAGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-4 TTAAGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-7 TTAAGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-6 TTAAGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-9 TTAAGAAAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-11 TTAAGAGAACACTTTGTGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-3 TTAAGAGAACACTTTGTGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-4 TTAAGAGAACACTTTGTGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-6 TTAAGAGAACACTTTGTGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-9 TTAAGAGAACACATTGTGAATAAAACAATAGTCTTTAATCACTCCTCA S1V5-7 TTAAGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA *** ** **** * *** ****** ***** ** ** ***
- Clones from subjects, regardless of visit, generally clustered together
- Exception of clones from subjects 1 and 2, which show some relationship to one another
- Clade with both strains present on tree
- Other clades are clustered by subject
- Exception of clones from subjects 1 and 2, which show some relationship to one another
- The phylogenetic tree suggests that there is no "rapid progression mutation"
- Subject 1 is a rapid progressor and Subject 2 is a nonprogressor
- They are closely related on the tree but show different progression rates
- Had there been a mutation coding for rapid progression on a specific location of the sequence, strains from the final visits of rapid progressors would be closely related to each other and not as closely related to nonprogressors
- Subject 1 is a rapid progressor and Subject 2 is a nonprogressor
Research Project Presentation
File:Bioinformatics Presentation 1.pdf
Scientific Conclusion
The purpose of this research project was to find a location or mutation on the env gene of HIV-1 that would differentiate rapid progressors from nonprogressors. Analysis of aligned sequences from the clones of strains from the first and last visits suggest that window 11 could be a favored location for mutations. Phylogenetic analysis suggests that there is no mutation that differentiates strains that cause rapid progression from those that result in nonprogression since strains clustered together by subject rather than progression. Future projects could look at window 11 in more depth, inducing mutations and tracking progression to see if it has an affect.
Acknowledgements
- My homework partner for the week was Drew Cartmel
- Drew and I worked together to develop and answer our research question
- Drew did half of the data collection for the project
- Drew worked on creating the graph used to present the data
- We worked together to analyse the data and come to the conclusion we did
- Kam D. Dahlquist, PhD gave the idea to present the S values in the way that we did
- This research project was based on and conducted with the results from Markham et al.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Jmenzago (talk) 23:56, 26 February 2020 (PST)
References
- Bedrock. (2020). Nucleotide Sequences. Retrieved February 20, 2020, from http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php
- Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., ... & Yu, X. F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences, 95(21), 12568-12573. doi: 10.1073/pnas.95.21.12568
- OpenWetWare. (2020). BIOL368/S20:Week 6. Retrieved February 20, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_6
- Phylogeny.fr. (2020). Retrieved February 20, 2020 from http://www.phylogeny.fr/.