README.md

hare-phylogenomics

Pipeline used for analyses of whole-exome data from 15 hare species and 2 outgroup rabbit species. We performed species tree inference, and estimated hybridization with species network inference and summary statistics (D-statistics, fraction of admixture, admixture proportion and f-branch statistics).

In each section bellow, I describe the pipeline used in a markdown file (follow links below). Scripts referenced in each section can be found inside the respective folders.

python scrips use python2.7.

Contact: mafaldasferreira (at) cibio.up.pt

Sections

1. Read processing, pseudoreferences and mapping
2. Calling genotypes and creating a consensus fasta
3. Species tree and ML whole exome tree
4. Divergence time inference (MCMCtree)
5. Discordance analyses between gene trees and species tree
6. Network analyses (PhyloNet and TreeMix)
7. Estimating divergence and diversity per species
8. Admixture analyses (D_min, f-branch, f_d, f_hom)

Links to the software used in this pipeline

Note: This is not an exhaustive list and some may be missing. All software should be also detailed in each section.

General data processing

• expHTS
• bwa
• samtools and bcftools
• Picard Tools
• Genome Analysis Toolkit
• bedtools

Pseudo-reference generation

• pseudo-it

Alignment processing

• AMAS
• TriFusion
• R package biomaRt
• snp-sites
• msa-split, from phast
• Genomics General

Phylogenomic or Population Genomic analyses

• ASTRAL-III
• RAxML
• PAUP* (implements SVDquartets)
• PAML (implements MCMCtree)
• SplitsTree4
• PhyloNet
• TreeMix
• Genomics General
• R package ape
• R package phangorn
• R package treeman