Skip to content

scripts used for the mitogenome paper of Cladoceran by Shao-Lin Xu

Notifications You must be signed in to change notification settings

ShaolinXU/Mitogenome_Branchiopoda

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

28 Commits
 
 
 
 
 
 

Repository files navigation

Mitogenome_Branchiopoda

scripts used for the mitogenome paper of Cladoceran by Shao-Lin Xu: Xu, S. L., Han, B. P., Martínez, A., Schwentner, M., Fontaneto, D., Dumon, H. J., & Kotov, A. A. (2021). Mitogenomics of Cladocera (Branchiopoda): marked gene order rearrangements and independent predation roots. Molecular Phylogenetics and Evolution, 107275.

Script

  1. code/iterative_metaspades_fishing.sh: extend seed sequence by iterative target assembly
    1. code/IMF_readme.md: readme file for iterative_metaspades_fishing.sh
  2. code/gcskwew.py: calculate compositional statistic of dna sequence (input as fasta format)
    1. this script was modified from SKewIT, all credit goes to the original author 1
  3. code/zorro.py: filter ambiguious align region
    1. This script was modified from Schwentner 2018 2

Data

  1. data/Appdendix.zip: all appdendix of this paper
  2. new 'matrix-7' data:
    1. data/OG_168.fa: amino acid sequence of 168 orthologous genes in the new 'matrix-7' in the paper
    2. data/OG_168.partition: the partition file of OG_168.fasta

Reference

1: Lu, Jennifer, and Steven L. Salzberg. "SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes." PLoS computational biology 16.12 (2020): e1008439.

2: Schwentner, M., S. Richter, D. C. Rogers, and G. Giribet. 2018. Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics. Proceedings of the Royal Society B: Biological Sciences 285:20181524.

About

scripts used for the mitogenome paper of Cladoceran by Shao-Lin Xu

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published