jdalapicolla

LanGen_pipeline_version2

Scripts in R for Landscape Genomics Analyses v.2

PopGenPipe

Population Genomics Pipeline used for SNPs data from VCF files.

SDM_biomod2

Scripts with comments in Portuguese for performing Species Distribution Models using MaxEnt in 'biomod2' package

LanGen_pipeline

Suit of R-scripts to perform landscape genomic analyses

LOCAL_ADAPTATION.R

Scripts in R for analyses of Identification of SNPs candidates and GEA and GPA studies - PART 4 in LANDSCAPE GENOMICS PIPELINE

Dalapicolla2019

Scripts and Suplemmentary Information used in the my Ph.D. thesis

IBD_models.R

Scripts in R for analyses of Isolation by Distance (IBD) - PART 2 in LANDSCAPE GENOMICS PIPELINE

SpeciesDelimitation

Scripts and Datasets for Phylogenomics of spiny rats - Genus Proechimys

BAG_SNPs

Script for estimating sample size for a germplasm/seeds bank (BAG) using allele frequency and genetic diversity of wild species/population based on SNPs

Bioinformatica

Pipelines e scripts para análises em Bioinformática

Coimbra-et-al-2021_CurrBiol

Code used to analyse WGS data of giraffe in Coimbra et al. 2021 (https://doi.org/10.1016/j.cub.2021.04.033)

Dalapicolla_Percequillo_2020

Species concepts and taxonomic practice in the integrative taxonomy era: an example using South American rodents

EXECT

fastStructure

A variational framework for inferring population structure from SNP genotype data.

Genomic-Consequences-of-Speciation-Reversal

genomic-data-analysis

Pipelines for analyzing genomic or transcriptomic data

ipyrad_to_BPP.R

Script to edit file .loci from ipyrad to run in BP&P

Isoetes_Scripts.R

Three-steps tutorial for filtering genomic data, estimating genetic structure, and calculating genetic diversity using a vcf

kratzert.github.io

my blog

lcwgs-guide-tutorial

MLPE.R

Scripts in R for analyses of Isolation by Resistance (IBR) - PART 3 in LANDSCAPE GENOMICS PIPELINE

Ne_StrataG.R

Script for estimating Effective Population Size (Ne) using Linkage Desequilibrium in StrataG package

ngsTools

Programs to analyse NGS data for population genetics purposes

Population_Connectivity

Pipeline to run analyses of Population Connectivity with a list of shared loci or haplotypes and Species Distribution Models

psmcr

R Port of psmc

r-markdown-tutorial

A short tutorial on using R + markdown

seqcap_pop

A pipeline for de novo assembly of population-level sequence capture datasets.

Surface-Metrics

tutorials

Tutorials on phylogenetic and phylogenomic inference

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis