README.md

numt_vertebrate

Scripts and software for NUMT identification and selection signals investigation.

File descriptions

• "numt_identification": scripts for NUMT, cNUMT identification
• "numt_selection": scripts for dcNUMT clustering and selection signals identification

Software requirement

Recommend to run on a multi-core workstation if many species are tested

OS requirement

• Linux: Ubuntu 20.04.6

Python dependencies

os
sys
Bio
Bio.Seq
time
pandas
re
numpy
collections
ete3
glob
Bio.Phylo.PhyloXML

Softwares requirement

• Genome download

  ncbi-genome-download

  https://github.com/kblin/ncbi-genome-download

• KaKs calculation

  KaKs_Calculator2.0

  https://sourceforge.net/projects/kakscalculator2/

• BLAST

  BLASTN v2.12.0+

  https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/

• Selection signal investigation

  paml4.9j

  https://github.com/abacus-gene/paml

• Sequence extractions

  BEDTools v2.26.0

  https://github.com/arq5x/bedtools2

• Reverse sequence

  revseq in EMBOSS v6.6.0.0

  https://emboss.sourceforge.net/

• Sequence alignments

  MAFFT v7.310

  https://mafft.cbrc.jp/alignment/software/source.html

• Rate of evolution

  BayesTraits v.4.0.1

  https://www.evolution.reading.ac.uk/BayesTraitsV4.0.1/BayesTraitsV4.0.1.html

• cdNUMT and mito genes tree reconstructions

  iqtree v2.0.3

  https://github.com/iqtree/iqtree2

• Clustered NUMT tree recontructions

  FastTree v2.1.11

  http://www.microbesonline.org/fasttree/

• Focal clade extraction

  Newick Utilities v1.7.0

  https://github.com/tjunier/newick_utils

Script download

wget https://github.com/chnyuch/numt_vertebrate.git

Instructions

Download the genomes, mito genomes and mito genes of focal species.

Identifying the NUMTs and identifying the cNUMTs.

Calculating the dNdS to identify dcNUMTs.

Clustering cNUMT and calculate the dNdS of clustered NUMTs and single NUMTs