CAFe to study phylogenetic relationships with whole genome sequences

[Malena Serrano Noreña]

I have a question for using the CAFe software. I want to look for phylogenetic relationships of some species of the caprinae subfamily. I have data of whole genome sequences for 8 animals belonging to 8 different species and other one as outgroup. My question is if with CAFé I can align the 9 whole genome assemblies and develope a phylogenetic analysis, of course under a LINUX environment.

[Tandy Warnow]

Dear Malena,

SATe is not designed for whole genome alignment. The issue is that whole
genomes evolve with rearrangements, duplications, and other events that
are incompatible with the assumption that the only evolutionary events
that occur are indels (insertions and deletions) and substitutions. If you
wish to perform whole genome alignments, you need to use other types of
software.

Tandy Warnow
http://tandy.cs.illinois.edu
Founder Professor of Bioengineering and Computer Science
The University of Illinois at Urbana-Champaign

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