Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

*********************************************** ALIGNMENTS Aligned single-copy orthologs from primate datasets obtained via NCBI. Alignments were performed using GUIDANCE2 with Mafft. An example of an alignment script is below. #!/bin/bash #PBS -k o #PBS -l nodes=1:ppn=8,vmem=40gb,walltime=45:00:00 #PBS -M [e-mail] #PBS -m abe #PBS -N 1_CODON_AlignQSUB #PBS -j oe cd /N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED for file in *unalign.fa; do dest="/N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED/"; f=${file%\_TRANS_unalign.fa}; /N/u/danvand/Carbonate/src/guidance.v2.02/www/Guidance/guidance.pl --seqFile "$dest""$file" --dataset "$f" --msaProgram MAFFT --out Order as_input --proc_num 10 --seqCutoff 0.93 --colCutoff 0.95 --seqType codon --bootstraps 60 --outDir $PWD; ## The above line runs the file through GUIDANCE2 which generates column and seq scores using 60 bootstrap replicates from MAFFT codon alignments. /N/u/danvand/Carbonate/bin/maskLowScoreResidues.pl "$f".MAFFT.aln.With_Names "$f".MAFFT.Guidance2_res_pair_res.scr "$f".GUIDANCE.MASK_SEQ.fa 0.93 nuc; ##The above line uses the scores file to mask low confidence residues /N/u/danvand/Carbonate/bin/trimal -in "$dest""$f".GUIDANCE.MASK_SEQ.fa -out "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa -gt 0.5 -cons 50; ##The above lineTrimAl to cut out sites not present in at least 50% of the taxa or conserved in 50% /N/u/danvand/Carbonate/pythonscripts/Clean.N.py "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa; ## The above line is just an adhoc fix because I realized Trimal was was counting the masked sequence and not trimming them. the easiest fix was to convert the N’s to gaps. /N/u/danvand/Carbonate/pythonscripts/remove_aln_gaps_update.pl "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa.NoNs.fa .5 .9 200 > "$dest""$f”_NO_GAP.fa; ## The above line now takes the new “gapped” sequence and deletes a site if more than 1/2 of the taxa don’t have, Masks the whole sequence if more than 10% of the sequence is missing or if it is under 200bp. /N/u/danvand/Carbonate/pythonscripts/ReplaceString.py "$f"_NO_GAP.fa "_.5_.9_200" "" "$f”_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa; ## The Above line just deletes fasta headerline annotation left from the previous script /N/u/danvand/Carbonate/pythonscripts/Remove_All_N_Taxa.py "$f”_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa; ## The Above line just takes out taxa that composed only of N’s, this turns out to matter and is more of a double check for all seqs before they are finalized. mv "$dest"*GUIDANCE* "$dest"../CODON_ALIGNED; rm "$dest"*MAFFT* "$dest"*Seqs* "$dest"COS* "$dest"END* "$dest"Sample* "$dest"log "$dest”*NO_GAP.fa ##The above lines just cut down build up and only keeps the most relevant last couple of steps, just in case you want to change something. You don’t have to realign everything. done; ***********************************************

ALIGNMENTS（比对分析）：通过NCBI（美国国家生物技术信息中心，National Center for Biotechnology Information）获取的灵长类数据集的单拷贝直系同源基因（single-copy orthologs）比对结果。本次比对采用GUIDANCE2结合MAFFT完成。以下为一段示例比对脚本：
#!/bin/bash
#PBS -k o
#PBS -l nodes=1:ppn=8,vmem=40gb,walltime=45:00:00
#PBS -M [e-mail]
#PBS -m abe
#PBS -N 1_CODON_AlignQSUB
#PBS -j oe
cd /N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED
for file in *unalign.fa; do
dest="/N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED/";
f=${file%_TRANS_unalign.fa};
/N/u/danvand/Carbonate/src/guidance.v2.02/www/Guidance/guidance.pl --seqFile "$dest""$file" --dataset "$f" --msaProgram MAFFT --out Order as_input --proc_num 10 --seqCutoff 0.93 --colCutoff 0.95 --seqType codon --bootstraps 60 --outDir $PWD;
## 上述命令通过GUIDANCE2处理该文件，该工具会基于MAFFT密码子序列比对生成的60次bootstrap（自展抽样）重复结果，计算列得分与序列得分。
/N/u/danvand/Carbonate/bin/maskLowScoreResidues.pl "$f".MAFFT.aln.With_Names "$f".MAFFT.Guidance2_res_pair_res.scr "$f".GUIDANCE.MASK_SEQ.fa 0.93 nuc;
## 上述命令利用得分文件对低置信度残基进行屏蔽。
/N/u/danvand/Carbonate/bin/trimal -in "$dest""$f".GUIDANCE.MASK_SEQ.fa -out "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa -gt 0.5 -cons 50;
## 上述命令使用TrimAl工具去除在至少50%的类群中未出现，或在50%的序列中不保守的位点。
/N/u/danvand/Carbonate/pythonscripts/Clean.N.py "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa;
## 上述命令为临时修复方案：因发现TrimAl会将屏蔽的序列计入统计并进行修剪，因此将序列中的N转换为间隙（gap）。
/N/u/danvand/Carbonate/pythonscripts/remove_aln_gaps_update.pl "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa.NoNs.fa .5 .9 200 > "$dest""$f"_NO_GAP.fa;
## 上述命令会执行以下过滤：若超过一半的类群在某一位点无有效序列，则移除该位点；若整条序列有超过10%的区域缺失，或序列长度低于200bp，则直接屏蔽整条序列。
/N/u/danvand/Carbonate/pythonscripts/ReplaceString.py "$f"_NO_GAP.fa "_.5_.9_200" "" "$f"_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa;
## 上述命令用于删除前序脚本在FASTA序列标题行中留下的注释信息。
/N/u/danvand/Carbonate/pythonscripts/Remove_All_N_Taxa.py "$f"_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa;
## 上述命令用于移除仅由N碱基组成的序列，该步骤为双重校验，确保最终序列均为有效序列。
mv "$dest"*GUIDANCE* "$dest"../CODON_ALIGNED;
rm "$dest"*MAFFT* "$dest"*Seqs* "$dest"COS* "$dest"END* "$dest"Sample* "$dest"log "$dest"*NO_GAP.fa;
## 上述命令用于清理冗余文件，仅保留最终相关的几步结果，以便后续需要调整流程时无需重新完成全部比对。
done;

搜集汇总

背景与挑战

背景概述

该数据集是灵长类系统发育基因组学研究的补充数据，旨在通过整合新组装的三个旧世界猴物种基因组和23个现有灵长类基因组，估计物种树和基因树，以解析灵长类进化关系中的争议分支和检测古老种间基因渗入事件。数据集包含对齐序列、基因树、分子定年数据集和相关分析脚本，支持系统发育和分子进化研究，数据文件格式多样（如NEXUS、树文件、压缩包），并附有详细的方法说明和关联文献引用。