Help With Whole Genome Alignment and phylogenetic tree

Question

[boramkim109]

I'm trying to compare whole genome (homology and unique difference) of three species and make phylogenetic tree (Apis mellifera, Drosophila melanogaster, Musca domestica).

But I'm new in this area..

I downloaded fasta files from Ensembl which contain the coding sequences (http://ftp.ensemblgenomes.org/pub/metazoa/release-54/fasta/).

But I'm not sure coding sequence file is the first step for above purpose.

1. How can I find the homology and unique difference between genomes? I'm looking for a tool or pipeline for it.

2. And do you usually make a phylogenetic tree with whole genome? Or do you make it with an orthologue? If I have to use sequence of one orthologous gene, then How can I choose the gene for three species?

[manaswwm]

In order to infer phylogenies through orthologs, I think the best way would be to choose a single species and find the orthologs of transcripts with the other two species, for finding orthologs you could use OrthoFinder, this way you could answer for example questions like 'Is Species "C" closer to species "A" than species "B"?' The alignments generated from aligning the orthologs could then be used as inputs for tools like HyPhy (or DataMonkey, an online server implementing HyPhy) that infers selection on phylogenies with alignments and also infer the phylogenetic trees