santiagosnchez

vcf2fasta

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

faSomeRecords

Extracts FASTA records from multiFASTA file based on a list of FASTA headers

gb2fasta

Perl script to convert GenBank records to FASTA format

rbh

Finds reciprocal-best-hit matches between two all-by-all BLAST searches

rBt

Handy functions for dealing with BEAST trees in R

somatic-mutation-analysis_bash_pipeline

PBS/torque-Bash pipeline for somatic and germline variant discovery and signature analysis

CompMap

Compares reads mapped to two reference and splits best alignments

ConcatFasta

Concatenates FASTA files, imputes dummy sequences, and prints a partition table

PolyFastA

Fast diversity estimator for FASTA sequences in Python

vcf2bayescan

It turns a VCF file into the input format for BayeScan; provided a tab-delimited population assignment file

CodonAlign

Generates a codon-based alignment from an amino acid alignment and CDS sequences

PolyVCF

Estimates nucleotide diversity on sliding windows from a VCF file

TreeTrimmer

Resolves paralogy on phylogenomic datasets using Robinson-Foulds distances

acc2gb

Shell code to retrieve GenBank records from a list of accession numbers (using gnu-parallel)

competitive_mapping_workflow

Pipeline and workflow for RNA-seq processing, differential expression and allele-specific expression analyses (and more).

DistKnKs

Calculates Kn/Ks distances from two CDS sequences

EEB214

Collection of jupyter notebooks for evolutionary biology remote learning

effective_number_of_codons

Calculates de number of effective codons Nc for an unaligned of coding sequences in FASTA format

extractGenBankToExcel

gdrive

Google Drive CLI Client

genetic_drift

Shiny app with a genetic drift simulator

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

Jellyfish

A fast multi-threaded k-mer counter

lastz-1

Program for aligning DNA sequences, a pairwise aligner.

lastzWrapper

Bash shell wrapper to build whole-genome alignments with lastz

microsatellites

R scripts and functions for microsatellite EBSP

MycoNet

paml_dist

SimCoalFastA

A neutral coalesent simulator that returns either a FASTA alignment, and SFS vector (csv), or a Newick genealogy

STRlength2repeat

Python code to convert STR length data to number of repetitions