This code_readme.txt file was generated on 2021-11-22 by Akhil Velluva


GENERAL INFORMATION

1. Title of Dataset: Data analysis pipeline and commands which are described in the article "Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow"

2. Author Information
A. Principal Investigator Contact Information
Name: Diana Le Duc
Institution: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
Address: 04103 Leipzig, Germany
Email: diana_leduc@eva.mpg.de

C. Alternate Contact Information
Name: Akhil Velluva
Institution: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
Address: 04103 Leipzig, Germany
Email: akhil_velluva@eva.mpg.de


DATA & FILE OVERVIEW

1. File List:

   Pipeline.txt : Step by step commands for analyzing the Sea Cow Genome

   snpAD.sh : Shell script for Genotyping of Sea cow individuals with snpAD tool

   Blast_Best_Hit.py : For extracting the best hit from the standalone blast out

   Match_Gene_From_Ensembel.awk : Intersect the ortho Ids between ensemble and The blast

   Merge_orthologus.awk : Merge The orthologous Lists

   kaks_codeml_lineage.pl :  calculation of ka/ks from orthologous genes

   FastaRead.pm : Perl module for reading fasta

   CodeMLPairwise.pm: Perl module to run kaks_codeml_lineage.pl

   mapping_common.py: python script match go ids from the exported file from Ensembl and orthos

   get.sig.go_Func.sh : Get significant genes from the GO analysis

   Pairwise_comparison.py : Count the number of differences within non overlapping blocks of 50 kb