| This repository contains large set of tools for analysing genome diversity developed by the Miller lab at PSU. |
hg clone https://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity
| Name | Version | Type | |
|---|---|---|---|
| eigensoft | 5.0.1 | package | |
| fisher | 0.1.4 | package | |
| gd_c_tools | 0.1 | package | |
| matplotlib | 1.2.1 | package | |
| mechanize | 0.2.5 | package | |
| networkx | 1.8.1 | package | |
| phast | 1.3 | package | |
| quicktree | 1.1 | package | |
| raxml | 7.7.6 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| : Group gene categories connected by shared genes | 1.0.0 | any | |
| : Convert from gd_snp or gd_genotype to VCF format, for submission to dbSNP | 1.1.0 | any | |
| : Fill in missing properties for a gd_snp or gd_genotype dataset | 1.1.0 | any | |
| : Examine sequence coverage for SNPs | 1.0.0 | any | |
| : Analyze the pedigree without genomic data | 1.0.0 | any | |
| : Map genomic intervals resembling specified source populations | 1.2.0 | any | |
| : Append summary columns for a population | 1.1.0 | any | |
| : Assess the enrichment/depletion of a gene set for GO terms | 1.1.0 | any | |
| : Discover familial relationships | 1.0.0 | any | |
| : Evaluate possible numbers of ancestral populations | 1.0.0 | any | |
| : CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype | 1.0.0 | any | |
| : Fetch DNA sequence for intervals surrounding the given SNPs | 1.0.0 | any | |
| : Show genetic relationships among individuals | 1.1.0 | any | |
| : pi, allowing for unsequenced intervals | 1.1.0 | any | |
| : prepare data for phylogenetic analysis | 1.1.0 | any | |
| : Select SNPs differentially cut by specified restriction enzymes | 1.0.0 | any | |
| : Assess the impact of a gene set on KEGG pathways | 1.2.0 | any | |
| : Build a gd_snp or gd_genotype file | 1.0.0 | any | |
| : Offspring estimated heterozygosity from a pedigree with sequenced founders | 1.0.0 | any | |
| : Principal Components Analysis of genotype data | 1.0.0 | any | |
| : π and θ | 1.0.0 | any | |
| : exchange rows in the above picture | 1.0.0 | any | |
| : Find suitable PCR primers for SNPs | 1.0.0 | any | |
| : Look up KEGG pathways for given Ensembl transcripts | 1.0.0 | any | |
| : Estimate the relative fixation index between two populations | 1.3.0 | any | |
| : show positions of SNVs and unsequenced intervals | 1.1.0 | any | |
| : Filter and convert to the format needed for these tools | 1.2.0 | any | |
| : Define a collection of individuals from a gd_snp dataset | 1.1.0 | any | |
| : Find high-scoring runs of SNPs | 1.1.0 | any | |
| : Offspring estimated heterozygosity of sequenced pairs | 1.0.0 | any | |
| : Compute a fixation index score for each SNP | 1.2.0 | any | |
| : Select a specified number of SNPs, uniformly spaced | 1.0.0 | any | |
| : construct a maximum-likelihood phylogenetic tree | 1.0.0 | any | |
| : Draw a KEGG pathway, highlighting specified gene modules | 1.1.0 | any | |
| : Characterize ancestries w.r.t. inferred ancestral populations | 1.0.0 | any | |
| : Assignment of optimal breeding pairs | 1.0.0 | any | |
| : Discard some SNPs based on coverage, quality or spacing | 1.2.0 | any | |