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.
code/iterative_metaspades_fishing.sh
: extend seed sequence by iterative target assemblycode/IMF_readme.md
: readme file foriterative_metaspades_fishing.sh
code/gcskwew.py
: calculate compositional statistic of dna sequence (input as fasta format)code/zorro.py
: filter ambiguious align region- This script was modified from Schwentner 2018 2
data/Appdendix.zip
: all appdendix of this paper- new 'matrix-7' data:
data/OG_168.fa
: amino acid sequence of 168 orthologous genes in the new 'matrix-7' in the paperdata/OG_168.partition
: the partition file ofOG_168.fasta
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.