Phylogenetic reconstruction and functional characterization of the ancestral Nef protein of primate lentiviruses

Supplementary data accompanying the manuscript "Phylogenetic reconstruction and functional characterization of the ancestral
Nef protein of primate lentiviruses".

• group_m_ancestry_consensus_gaps_removed.afa - consensus amino acid sequences for ancestral reconstructions at the six internal nodes in FASTA format
• node35.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions at the root of the primate lentivirus phylogeny (node 35) for 1,000 trees sampled from the posterior distribution
• node51.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVsun (node 51) for 1,000 trees sampled from the posterior distribution
• node52.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpz (node 52) for 1,000 trees sampled from the posterior distribution
• node55.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpzptt (node 55) for 1,000 trees sampled from the posterior distribution
• node56.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 groups M and N and SIVcpzptt (node 56) for 1,000 trees sampled from the posterior distribution
• node59.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 group M (node 59) for 1,000 trees sampled from the posterior distribution