Extra Multiple Sequence Alignment

Try to perform a small MSA

Multiple sequence alignment (more here) leads to the identification of the homologous regions in a set of sequences, and to the "edit paths" from one sequence to another.

The tools

There are different options for MSA, and the ideal choice might depend on the nature of the dataset (sequence size, dataset size, nucleotide or protein...) and a good summary of the available options is in this review here

During the workshop we will use:

• MAFFT for MSA
• IQTree for tree reconstruction

The file formats: MSA

A common output format is "FASTA with gaps":

>seq1
--CAGTCGATCGGTAGCAGCTGACGTAGCAG--GAAGCT
>seq2
GGCAGTCGATC-GTAGCAGCTGACGTAGCAG--GAAGCT
>seq3
--CAGTCGATCGGTAGCAGCTGACGTAGCAG--CTAGC-

Another popular format is Phylip. The format was originally defined and used in Joe Felsenstein’s PHYLIP package.

      5    42
Turkey    AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT
Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT
H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA
Chimp     AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT
Gorilla   AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA