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

本补充数据附于论文《灵长类慢病毒祖先Nef蛋白的系统发育重建与功能表征》。
group_m_ancestry_consensus_gaps_removed.afa：采用FASTA（FASTA）格式存储的6个内部节点祖先重建结果的一致性氨基酸序列。
node35.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对灵长类慢病毒系统发育树根节点（节点35）的祖先氨基酸序列重建结果进行的多序列比对文件。
node51.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对HIV-1与SIVsun的共同祖先（节点51）的祖先氨基酸序列重建结果进行的多序列比对文件。
node52.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对HIV-1与SIVcpz的共同祖先（节点52）的祖先氨基酸序列重建结果进行的多序列比对文件。
node55.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对HIV-1与SIVcpzptt的共同祖先（节点55）的祖先氨基酸序列重建结果进行的多序列比对文件。
node56.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对HIV-1 M组、N组与SIVcpzptt的共同祖先（节点56）的祖先氨基酸序列重建结果进行的多序列比对文件。
node59.fa.mafft：针对从后验分布中抽样得到的1000棵系统发育树，对HIV-1 M组共同祖先（节点59）的祖先氨基酸序列重建结果进行的多序列比对文件。