KP Ramirez Week 5: Difference between revisions
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*All the individual branches on the unrooted tree indicated how far they were on the branches, those were more divergent with longer branches then shorter. | *All the individual branches on the unrooted tree indicated how far they were on the branches, those were more divergent with longer branches then shorter. | ||
*S was counting every base pair that was different from the multiple sequence alignment. There were 25 sequences. | *S was counting every base pair that was different from the multiple sequence alignment. There were 25 sequences. | ||
S is going to tell you DIVERSITY. Its a rough estimate of how different those sequences are from each other. | *S is going to tell you DIVERSITY. Its a rough estimate of how different those sequences are from each other. | ||
Then you calculate θ. Defined as the average genetic pairwise difference. It indicates the average genetic pairwise difference between two sequences. You can get an absolute number of the pair of differences. So we wanna know what is the average differences between the two sequences. θ is an estimate. So we take the S value and divide it by the harmonic sum. | Then you calculate θ. Defined as the average genetic pairwise difference. It indicates the average genetic pairwise difference between two sequences. You can get an absolute number of the pair of differences. So we wanna know what is the average differences between the two sequences. θ is an estimate. So we take the S value and divide it by the harmonic sum. | ||
*The last measure was to look at the minimum and maximum differences through the clustdist tool. This created a pairwise distance matrix. The distance matrix is to find the lowest number that is not 0. You have to look for the smallest distance between the sequences. You had to import the data from subjects to find the min and max between the two subjects. | *The last measure was to look at the minimum and maximum differences through the clustdist tool. This created a pairwise distance matrix. The distance matrix is to find the lowest number that is not 0. You have to look for the smallest distance between the sequences. You had to import the data from subjects to find the min and max between the two subjects. | ||
{{Kevin A Paiz-Ramirez}} | {{Kevin A Paiz-Ramirez}} | ||
Revision as of 09:45, 16 February 2010
Notes for my benefit
Divergence and diversity
- Divergence is how different are the sequences are from each other. If you have 10 sequences and 1 is different. They are not very divergent because they are only different by one. If you have like say 10 bp differences then they are very divergent.
- All the individual branches on the unrooted tree indicated how far they were on the branches, those were more divergent with longer branches then shorter.
- S was counting every base pair that was different from the multiple sequence alignment. There were 25 sequences.
- S is going to tell you DIVERSITY. Its a rough estimate of how different those sequences are from each other.
Then you calculate θ. Defined as the average genetic pairwise difference. It indicates the average genetic pairwise difference between two sequences. You can get an absolute number of the pair of differences. So we wanna know what is the average differences between the two sequences. θ is an estimate. So we take the S value and divide it by the harmonic sum.
- The last measure was to look at the minimum and maximum differences through the clustdist tool. This created a pairwise distance matrix. The distance matrix is to find the lowest number that is not 0. You have to look for the smallest distance between the sequences. You had to import the data from subjects to find the min and max between the two subjects.
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