Griffitts:Phylogenetics
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Alignment
MUSCLE
- Go to the MUSCLE website
- Paste your sequences in FASTA format with two returns between each one
- To generate FASTA format from Strider, select File and then Export as…; when the new window pops up, set the Format bar to FASTA
- Set the output to "Pearson/FASTA"
- Do NOT change any of the other parameters
- Hit Submit
- When you have the alignment, click on the Result Summary tab
- Right click on the link beneath Alignments in FASTA format and select Save link as…
- Give the file the name that you want and then add the extension .txt
ALTER
- Go to the ALTER website
- Under 1. Select format
- Choose "MUSCLE" for program
- Choose "FASTA" for format
- Under 2. Paste or Upload MSA hit upload…
- Navigate to the .txt file that you created using MUSCLE, select it, and hit open
- Under 3. Select output format and convert
- Choose "PAUP" for program
- Choose "NEXUS" for format
- Hit Convert!
- Under 4. Save converted MSA hit save… and then Okay
- Open the .nex file with a text editor
- On the sixth line down delete where it says
match=.
- Scroll to the bottom and paste the following[1] after
end;
:Begin paup;
set autoclose=yes;
set criterion=parsimony;
set root=outgroup;
set storebrlens=yes;
hsearch addseq=random nreps=1000 swap=tbr hold=1;
showtree;
End; - Save
NOTE: If you're doing this with multiple alignments, you'll have to refresh the ALTER page before working on a new .txt file.
Trees
Notes
[1] See https://lswiki.byu.edu/index.php/Life_Sciences_Wiki:Community_Portal.