Griffitts:Phylogenetics

Alignment

To start off, you need to perform an alignment of all your sequences. This can be done using MUSCLE. The output file (.txt) then needs to be converted to a .nex file, which can be done using ALTER.

MUSCLE

1. Go to the MUSCLE website
2. 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
3. Set the output to "Pearson/FASTA"
4. Do NOT change any of the other parameters
5. Hit Submit
6. When you have the alignment, click on the Result Summary tab
7. Right click on the link beneath Alignments in FASTA format and select Save link as…
8. Give the file the name that you want and then add the extension .txt

ALTER

1. Go to the ALTER website
2. Under 1. Select format
   • Choose "MUSCLE" for program
   • Choose "FASTA" for format
3. Under 2. Paste or Upload MSA hit upload…
4. Navigate to the .txt file that you created using MUSCLE, select it, and hit open
5. Under 3. Select output format and convert
   • Choose "PAUP" for program
   • Choose "NEXUS" for format
6. Hit Convert!
7. Under 4. Save converted MSA hit save… and then Okay
8. Open the .nex file with a text editor
9. On the sixth line down change

   interleave datatype=NUCLEOTIDE gap=- match=.;

   to

   interleave datatype=NUCLEOTIDE gap=-;

10. Scroll to the bottom and change

    ;
end;

    to the following^[1]:

    ;
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;

11. 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.

Notes

[1] See https://lswiki.byu.edu/index.php/Life_Sciences_Wiki:Community_Portal.