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
NOTE: At this point you can view your aligned sequences in MacClade.
 * 1) Go to the MUSCLE website
 * 2) Paste your sequences in FASTA format with two returns between each one
 * 3) * To generate FASTA format from Strider, select File and then Export as…; when the new window pops up, set the Format bar to FASTA
 * 4) Set the output to "Pearson/FASTA"
 * 5) Do NOT change any of the other parameters
 * 6) Hit Submit
 * 7) When you have the alignment, click on the Result Summary tab
 * 8) Right click on the link beneath Alignments in FASTA format and select Save link as…
 * 9) Give the file the name that you want and then add the extension .txt

ALTER
NOTE: If you're doing this with multiple alignments, you'll have to refresh the ALTER page before working on a new .txt file.
 * 1) Go to the ALTER website
 * 2) Under 1. Select format
 * 3) * Choose "MUSCLE" for program
 * 4) * Choose "FASTA" for format
 * 5) Under 2. Paste or Upload MSA hit upload…
 * 6) Navigate to the .txt file that you created using MUSCLE, select it, and hit open
 * 7) Under 3. Select output format and convert
 * 8) * Choose "PAUP" for program
 * 9) * Choose "NEXUS" for format
 * 10) Hit Convert!
 * 11) Under 4. Save converted MSA hit save… and then Okay
 * 12) Open the .nex file with a text editor
 * 13) At the top of the file, change "" to ""
 * 14) Scroll to the bottom and change ""to the following[1]:""
 * 15) Save

PAUP
NOTE: PAUP has a command-line interface. A .pdf user manual is available here and a .pdf command line reference manual is available here.
 * 1) Open PAUP
 * 2) Move the file(s) you intend to analyze into the same folder as the PAUP executable file
 * 3) * e.g. if PAUP is on the desktop, then move your .nex file(s) to the desktop, too
 * 4) Use the   ("change directory") command to navigate to PAUP
 * 5) * e.g.
 * 6) Use the   command to analyze your .nex file
 * 7) * e.g.

MacClade

 * 1) Open MacClade
 * 2) Select the alignment file
 * 3) * e.g.
 * 4) Click on the Windows menu
 * 5) Select Tree Window
 * 6) Select Open Treefile&hellip;
 * 7) Load your saved tree file
 * 8) * e.g.

FigTree

 * 1) Open FigTree
 * 2) Load your saved tree file
 * 3) * e.g.