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generating a phylogeny tree

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?

genome gene alignment sequence r
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updated by Mensur Dlakic Mensur Dlakic • written by a4appy23 • a4appy23

2 answers

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/

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written by Mensur Dlakic Mensur Dlakic

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.

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written by h.mon h.mon

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