quentinrougemont Goto Github PK

abc_4pop

ABC analysis to investigate speciation by using genomics data from four populations allowing for genomic heterogeneities in Ne and M

abc_inferences

abc_inferences_data

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

coho_ldscp_genomics

scripts to reproduce our landscape genomics results in coho salmon

coho_salmon_recomb

LDHAT estimates of population effective recombination rates from WHS coho salmon data

demographicinference

Scripts to compare models of divergence using diffusion approximation (dadi)

dils_4pop

pipeline for model comparisons and parameter estimates, for 3 alternative topologies involving 4 populations

fine_structure

fsc_modelling

multi-population modeling of divergence history based on fastsimcoal

fwd_sims

Pipeline for forward simulation of admixture under different evolutionary scenario

gatk_haplotype

gbs_synonymy_with_genome

Find synonymy of SNP variants from GBS

genome_annotation

genome annotation (RNAseq and TE) pipeline (draft)

genome_assembly

generate genome assembly with hifi

ldhat_workflow

linkmap_workflow

set of scripts to generate linkage map with LepMap3

marine_ibm_paper

script based on Matz et al. 2020. Simple modifications to guide slim users

microsatdemoginference

Contains Script To performed Demographic inference using microsatelittes data with coalescent theory, ABC model selection and parameter estimation. I also explore the use of Random Forest for model selection.

mscalcfst

simple Fst/pi calculator from ms (2 pops only)

msnsam

Hudson's ms with variable sample size across loci

ont_assembly

pipeline to assemble genome from long read, correct with short read (and evaluate quality)

pinpis

computation of piN/piS for WGS/GBS data

poolseq_workflow

rad_pe_workflow

radseqanalysis

sed_cheatsheet

selection_efficacy

scipt to reproduce our work on Coho WGS

singletons_analysis

slim_heliconius