santiagosnchez Goto Github PK
Name: Santiago Sanchez-Ramirez
Type: User
Santiago Sanchez-Ramirez's Projects
poly-div_sfs
Estimates polymorphism and divergence parameters from FASTA alignments
polyfasta
Fast diversity estimator for FASTA sequences in Python
polyvcf
Estimates nucleotide diversity on sliding windows from a VCF file
rbh
Finds reciprocal-best-hit matches between two all-by-all BLAST searches
rbt
Handy functions for dealing with BEAST trees in R
rplotebs
Plots the CSV files from the Extended Bayesian Skyline Plot model in BEAST
runcs
R function to run CIRCUITSCAPE from an R console on Mac/Linux
simcoalfasta
A neutral coalesent simulator that returns either a FASTA alignment, and SFS vector (csv), or a Newick genealogy
sing_snp_vcf
Reports a single SNP per chromosome/contig/scaffold/locus either randomly or the one with the highest minor allele frequency
somatic-mutation-analysis_bash_pipeline
PBS/torque-Bash pipeline for somatic and germline variant discovery and signature analysis
strlength2repeat
Python code to convert STR length data to number of repetitions
treetrimmer
Resolves paralogy on phylogenomic datasets using Robinson-Foulds distances
vcf2bayescan
It turns a VCF file into the input format for BayeScan; provided a tab-delimited population assignment file
vcf2colony
Converts a VCF file into an input file for Colony2
vcf2fasta
Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file
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