Readme of ParaAT (Oct. 4, 2014; version 2.0) 1. Before running Please make sure the following programs are put into the global directory and can be accessible from any working directory. (1) ParaAT.pl; (2) Epal2nal.pl; (3) Multiple sequence aligner (clustalw2 | t_coffee | mafft | muscle). Sequence IDs in amino acid file, nucleotide file, and homologous group file should be the same. 2. How to run The test is on a small dataset containing 100 human-mouse orthologs. test.cds: coding sequences for human and mouse test.pep: protein sequences for human and mouse test.homologs: 100 pairs for human-mouse orthologs proc: number of processors, which is set at 6 and allowable for change during running The command to run on this dataset is: ParaAT.pl -h test.homologs -n test.cds -a test.pep -p proc -o output For help information and details parameter setting, please type: ParaAT.pl -help 3. Download & Update Please visit <http://cbb.big.ac.cn> for downloads and updates. 4. Contact information Zhang Zhang, Ph.D. CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics, Chinese Academy of Sciences (CAS) No.1 Beichen West Road Chaoyang District, Beijing 100101 China Email: zhangzhang@big.ac.cn Tel.: +86(10)8409-7261 Fax: +86(10)8409-7845 Web: http://cbb.big.ac.cn This is a modified version! I modified the naming to fit the linux naming restrictions. 20230416