I have a bunch of genes and a phylogeny of ten species. I want to reconstruct the phylogenetic profile for all of the ten genes and know for how each gene is lost in different lineages in batch. Is there a software for this purpose?
MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. MEGA is used by biologists in a large number of laboratories for reconstructing the evolutionary histories of species and inferring the extent and nature of the selective forces shaping the evolution of genes and species
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version 2.3.6
You are likely looking for an ortholog detection pipeline. See here What Is The Best Method To Find Orthologous Genes Of A Species? for an overview, as you are looking for gene-absence, you need to detect presence first. Likely, you can get orthologs in a matrix for all genes in 10 organisms.