Sequence Alignment for Phylogenetic Analysis: Difference between revisions

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 == Locate Sequences and Generate FASTA File ==
+=== Generating a FASTA File===
+* FASTA format is described [https://zhanglab.ccmb.med.umich.edu/FASTA/ here], and [https://en.wikipedia.org/wiki/FASTA_format 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:
+<code>
+>SEQUENCE_1
+MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
+LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
+IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
+MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
+>SEQUENCE_2
+SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
+ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
+</code>
+* Save sequences in notepad, [https://notepad-plus-plus.org/ notepad++] or [https://www.sublimetext.com/ 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 [https://www.ncbi.nlm.nih.gov/refseq/ RefSeq mRNA].  If there are multiple mRNA's for the gene, name them
 == Create Multiple Sequence Alignment using CLUSTAL Omega ==
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 * Generate phlogenetic trees with [http://megasun.bch.umontreal.ca/People/lartillot/www/download.html PhyloBayes] or  Mr. Bayes [[Using Mr Bayes to For Phlyogenetic Analysis]].
-=== PhyloBayes Analysis ==
+=== PhyloBayes Analysis ===
 * Mark in your notes the software version used.
 * The PhyloBayes manual can be found [http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes4.1.pdf here].