Sequence Alignment for Phylogenetic Analysis

Locate Sequences and Generate FASTA File

Generating a FASTA File

• FASTA format is described here, and here you need each sequence to start with a >SEQUENCENAME followed by a return and then the sequence, in this case the protein sequence. An example of a FASTA file would be:

>SEQUENCE_1

MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG

LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK

IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL

MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL

>SEQUENCE_2

SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI

ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

• Save sequences in notepad, notepad++ or sublime (not Word) as a <FILENAME>.fasta file.
• Sequence names cannot have spaces. Generally its better to name it as mm_Gdf15-NM_004864.4 where mm indicates mouse, Gdf15 is the gene name and NM indicates a RefSeq mRNA. If there are multiple mRNA's for the gene, name them

Create Multiple Sequence Alignment using CLUSTAL Omega

• CLUSTAL Omega is available at https://www.ebi.ac.uk/Tools/msa/clustalo/
• Select output format NEXUS to import into Mr Bayes or PHYLIP format to import into PhyoBayes
• Generate phlogenetic trees with PhyloBayes or Mr. Bayes Using Mr Bayes to For Phlyogenetic Analysis.

PhyloBayes Analysis

• Mark in your notes the software version used.
• The PhyloBayes manual can be found here.