generating a phylogeny tree

Question

[a4appy23]

Hi, I have whole genome data of few species of whales.i need to create a phylogeny tree any suggestion on how should i proceed?

Answer 1

[Mensur Dlakic]

To what @h.mon suggested I would add a trimming step between alignment and concatenation.

Busco https://busco.ezlab.org/

Cetartiodactyla https://busco.ezlab.org/frames/vert.htm

MAFFT https://mafft.cbrc.jp/alignment/software/

Trimming https://github.com/scapella/trimal

Concatenation https://github.com/qiyunzhu/BeforePhylo

IQ-TREE http://www.iqtree.org/

Answer 2

[h.mon]

From each genome, get single copy mammals (or maybe Cetartiodactyla) orthologs with BUSCO, align each set of genes with MAFFT or MUSCLE, then estimate a phylogeny on the concatenated alignment with IQTree. Depending on how close or distant the species are, using predicted proteins (aminoacids) or gene (nucleotides) will be better.