/CASTER-data

Scripts for generating data and figures for CASTER paper

Primary LanguageMathematicaMIT LicenseMIT

CASTER: Direct species tree inference from whole-genome alignments

Scripts for generating data and figures

Proof

Mathmatica script to verify the correctness of Proposition 2

Simulated

Simulated datasets

Quartet

Scripts for Quartet dataset

  • SimulationScript: MSPrime scripts to simulate quartet phylogenies

  • BPP_ControlFiles: Templates for BPP control files

  • IntrogressionSignal: Implementation for parsimony-based introgression signal detection for quartets (ABBA-BABA test)

  • FigureScripts: Script and data for generating Figure 2 and related figures

SR201_SR21_S101

Scripts for SR201 dataset, SR21 dataset, and S101 datset

  • SimulationScript: MSPrime scripts to simulate SR201 and SR21 phylogenies

  • FigureScripts: Script and data for generating Figure 3 and related figures

Biological

Scripts used in biological datasets

Mammal241

Foley et al. placental mammal dataset

  • Phylogeny: whole-genome phylogenies and per-chromosome phylogenies by CASTER-site

  • SlidingWindow: Script and data for generating Figure 4 and related figures for sliding window analysis

Bird363

Stiller et al. bird dataset

  • Phylogeny: Input file list and output phylogenies of CASTER-site

  • SlidingWindow: Script and data for generating Figure 5 and related figures

Others

Relavent scripts used in other biological datasets

Commands

CASTER (site and pair):

$PROGRAM_NAME -C -t $THREADS $MSA

wASTRAL (gene trees):

raxml-ng --msa $MSA --model GTR+G --threads 1
iqtree2 -s $MSA -te $MSA.raxml.bestTree -m GTR+G4 -abayes -nt 1

wASTRAL (species tree):

astral-hybrid -B -C -t $THREADS $GENE_TREES

ASTRAL (species trees):

astral -C -t $THREADS $GENE_TREES

SVDQuartets (haploid, single individual):

svdquartets nthreads=$THREADS evalQuartets=all seed=5000

SVDQuartets (unphased diploid):

svdquartets nthreads=$THREADS evalQuartets=random nquartets=105597360 taxpartition=species seed=5000

SVDQuartets (multiple individuals):

svdquartets nthreads=$THREADS evalQuartets=all taxpartition=species seed=5000

RAxML-ng (haploid, single individual):

raxml-ng --tree pars{1} --msa $MSA --model GTR+G --threads $THREADS

RAxML-ng (unphased diploid):

raxml-ng --tree pars{1} --msa $MSA --model GTGTR4+G --threads $THREADS

RAxML-ng (multiple individuals):

raxml-ng --tree pars{1} --msa $MSA --model GTR+G --threads $THREADS --tree-constraint $SPECIES_DELIMITATION

Placental mammal whole genome alignment:

caster-site -C -t 64 -o chr1.nw chr1.fa
caster-site -r 0 -s 0 -t 128 -f list -g chr1.nw -o whole_genome.nw chr_list.txt