POSTGRADUATE COURSE

Software

TITLE	DESCRIPTION
ANGSD	Analysis of Next Generation Sequencing Data
Astral	Accurate Species tree algorithm
BayPass	Population genomics software which is aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates
BLAST	Basic Local Alignment Search Tool
Bowtie2	ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
BPP	Bayesian species delimitation using multilocus sequence data
CD-HIT	clustering and comparing protein or nucleotide sequences.
Clustal-Omega	program that uses seeded guide trees and HMM profile-profile techniques to generate multiple sequence alignments
DnaSP 6	Análisis de Variación Genética; Flujo Génico; Coalescencia
Fastsimcoal2	Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models
GMYC	Generalized Mixed Yule Coalescent
Hmmer	biosequence analysis using profile hidden Markov models
IQTREE	Efficient software for phylogenomic inference
Mafft	Programa de alineamiento múltiple de aminoácidos o secuencias de nucleótidos
Momi2	Software for demographic history
mPTP	Species delimitation using the multi-rate Poisson Tree Processes
OrthoFinder	Accurate inference of orthologs, orthogroups, the rooted species, gene trees and gene duplication events
PartitionFinder2	Software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses
Phylomedb	Public database for complete catalogs of gene phylogenies (phylomes)
RevBayes	Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language
Samtools	Sequence alignment/mapping tool
Selscan	Haplotype based scans for selection
SLIM3	Software for population genetics simulations
TNT	Program for phylogenetic analysis under parsimony
Tracer	Programa para el análisis de los archivos de traza generados por método Bayesiano MCMC
TrimAL	Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
Trimmomatic	Read trimming tool for NGS data
Trinity	RNAseq de novo assembly

Mas Software \| por Joe Felsenstein (University of Washington)
Mas Software \| por S. O. Kolokotronis (American Museum of Natural History)