MSA of single copy gene sequences using OrthoVenn2 output

Question

[shanewidanagama]

Hello,

This is my first time doing comparative analyses like orthologous gene clustering and phylogenetic tree construction. Using the output of OrthoVenn2, how can I perform multiple sequence alignment of the proteins of single-copy genes for the purpose of phylogenetic tree construction? The online version of OrthoVenn2 produces a webpage listing all single-copy gene clusters, but not their sequences. Assuming I acquire all the protein sequences, I am also not sure of how to perform hundreds of alignments (for each of the single copy genes). I am trying to perform MSA using mafft, but anything works.