eead-csic-compbio

allopolyploids

PhyloSD: Phylogenomic Subgenome Detection pipeline

barley-agroclimatic-association

Association with high-resolution climate data reveals selection footprints in genomes of barley landraces across the Iberian peninsula

barley_pangenes

Clusters of gene models or alleles found in barley assemblies in a similar genomic location

bioinformatics

Bioinformatics resources and best-practices for beginners

chloroplast_assembly_protocol

A set of scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads

get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

metagenome_Pfam_score

Protocol for finding informative protein families and then using them to score metagenomic sets.

scripting_linux_shell

A collection of recipes to start scripting in the linux command line

plant-scripts

Scripting analyses of genomes in Ensembl Plants

get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

eead-csic-compbio/get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

eead-csic-compbio/chloroplast_assembly_protocol

A set of scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads

eead-csic-compbio/metagenome_Pfam_score

Protocol for finding informative protein families and then using them to score metagenomic sets.

eead-csic-compbio/allopolyploids

PhyloSD: Phylogenomic Subgenome Detection pipeline

eead-csic-compbio/bioinformatics

Bioinformatics resources and best-practices for beginners

eead-csic-compbio/scripting_linux_shell

A collection of recipes to start scripting in the linux command line

eead-csic-compbio/primers4clades

Automated pipeline for the design of PCR primers for cross-species amplification of novel sequences

eead-csic-compbio/barley-agroclimatic-association

Association with high-resolution climate data reveals selection footprints in genomes of barley landraces across the Iberian peninsula

eead-csic-compbio/bioinformatica_estructural

Este material presenta algunos algoritmos para el estudio de la estructura molecular de proteínas y ácidos nucleicos. Introduce problemas (y estrategias para resolverlos) desde la estructura primaria a la cuaternaria. A lo largo hay referencias a artículos y ejercicios que a veces requieren conocimientos de programación.

eead-csic-compbio/coexpression_motif_discovery

Discovering cis-regulatory motifs in proximal promoters of plants in RSAT::Plants

eead-csic-compbio/vcf-filter

Java tool to filter an input VCF file a la carte, based on HTSJDK and Apache commons CLI.

eead-csic-compbio/barleyGO

Software to annotate barley sequences with Gene Ontology terms

eead-csic-compbio/EEADannot

Manual curation of selected DNA motifs and cis regulatory sites, mostly from plants

eead-csic-compbio/split_pairs

split_pairs.pl is a simple and efficient utility for pre-processing NGS sequence reads in FASTQ and FASTA formats, suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions

eead-csic-compbio/barley_pangenes

Clusters of gene models or alleles found in barley assemblies in a similar genomic location

eead-csic-compbio/bioconda-recipes

Conda recipes for the bioconda channel.

eead-csic-compbio/biostats_bioinfo

Source code of teaching material for the course Biostatistics and Bioinformatics

eead-csic-compbio/eead-csic-compbio.github.io

Website source of the Computational & Structural Biology group @EEAD-CSIC

eead-csic-compbio/footprintDBclient

Query footprintDB from the command-line

eead-csic-compbio/kmeleon

Pipeline for k-mer count analysis of genomic diversity

eead-csic-compbio/methods_biostats_bioinfo

Sample data and source code used in the course "Methods in biostatistics and bioinformatics"

eead-csic-compbio/perl_bioinformatica

eead-csic-compbio/phg_v2

PHG version 2

eead-csic-compbio/plantoquimica

Paseo bioquímico y genómico en el jardín botánico

eead-csic-compbio/prunusmap_web

This is the web interface of prunusmap, which uses an evolved barleymap search engine

eead-csic-compbio/subopt-kaks

Suboptimal alignments and Ka, Ks calculations

eead-csic-compbio/vcf2alignment

Protocol to produce multiple sequence alignments out of VCF files which can be used for phylogenetic tree construction.