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ucsc-pslsortacc
|
public |
Remove chain-breaking alignments from chains that break nested chains.
|
2024-12-12 |
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python-hyphy-python
|
public |
HyPhy package interface library
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2024-12-12 |
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fastsimbac
|
public |
Models bacterial recombination
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2024-12-12 |
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selam
|
public |
Simulation of Epistasis Local adaptation, with Ancestry and Mate choice
|
2024-12-12 |
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ucsc-catdir
|
public |
concatenate files in directory to stdout.
|
2024-12-12 |
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ucsc-fatotab
|
public |
convert fa file to tab separated file
|
2024-12-12 |
|
ucsc-getrnapred
|
public |
Get virtual RNA for gene predictions
|
2024-12-12 |
|
aprfinder
|
public |
Tool for finding aphased repeats.
|
2024-12-12 |
|
r-loom
|
public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.
|
2024-12-12 |
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ucsc-mafsplit
|
public |
Split multiple alignment files
|
2024-12-12 |
|
snp-dists
|
public |
Convert a FASTA alignment to SNP distance matrix
|
2024-12-12 |
|
rmath4
|
public |
standalone Rmath library from R
|
2024-12-12 |
|
mappy
|
public |
Minimap2 Python binding
|
2024-12-12 |
|
ucsc-pslmap
|
public |
map PSLs alignments to new targets using alignments of
|
2024-12-12 |
|
pin_hic
|
public |
A Hi-C scaffolding method
|
2024-12-12 |
|
ucsc-psltobed
|
public |
transform a psl format file to a bed format file.
|
2024-12-12 |
|
r-soap-nmr
|
public |
No Summary
|
2024-12-12 |
|
ucsc-crtreeindexbed
|
public |
Create an index for a bed file.
|
2024-12-12 |
|
mlrho
|
public |
Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate.
|
2024-12-12 |
|
ucsc-bedgeneparts
|
public |
Given a bed, spit out promoter, first exon, or all introns.
|
2024-12-12 |
|
nemo-age
|
public |
In Nemo-age, it is possible to model genetic and phenotypic evolution in populations with, for instance, overlapping generations, a seed bank, and multiple age classes with stage-specific transition rates, fecundities, selection pressures, and dispersal rates, among other things.
|
2024-12-12 |
|
seq-gen
|
public |
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.
|
2024-12-12 |
|
phyx
|
public |
Phylogenetics tools for linux (and other mostly posix compliant) computers
|
2024-12-12 |
|
ucsc-pslmappostchain
|
public |
Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues.
|
2024-12-12 |
|
orientagraph
|
public |
OrientAGraph enables Maximum Likelihood Network Orientation (MNLO), as a standalone routine or as a search heuristic within TreeMix, a popular package for estimating admixture graphs from f-statistics (or related quantities).
|
2024-12-12 |
|
tidyp
|
public |
Program for cleaning up and validating HTML
|
2024-12-12 |
|
ucsc-psltopslx
|
public |
Convert from psl to pslx format, which includes sequences
|
2024-12-12 |
|
perl-heap-simple-xs
|
public |
No Summary
|
2024-12-12 |
|
py_fasta_validator
|
public |
Simply and quickly validate a fasta file. Invalid files return non-zero exit codes
|
2024-12-12 |
|
ucsc-gaptolift
|
public |
create lift file from gap table(s)
|
2024-12-12 |
|
mseqtools
|
public |
fastq/fasta file manipulation toolkit
|
2024-12-12 |
|
adapterremoval
|
public |
The AdapterRemoval v2 tool for merging and clipping reads.
|
2024-12-12 |
|
malder
|
public |
MALDER is a version of ALDER (http://groups.csail.mit.edu/cb/alder/) that has been modified to allow multiple admixture events.
|
2024-12-12 |
|
ucsc-bigwigcat
|
public |
merge non-overlapping bigWig files
|
2024-12-12 |
|
ucsc-pslselect
|
public |
select records from a PSL file.
|
2024-12-12 |
|
ucsc-bigwigmerge
|
public |
Merge together multiple bigWigs into a single output bedGraph.
|
2024-12-12 |
|
ucsc-pslmrnacover
|
public |
Make histogram of coverage percentage of mRNA in psl.
|
2024-12-12 |
|
poplddecay
|
public |
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format (VCF) files.
|
2024-12-12 |
|
fusioncatcher-seqtk
|
public |
This is modified Seqtk version required for FusionCatcher.
|
2024-12-12 |
|
gsalign
|
public |
GSAlign: an ultra-fast sequence alignment tool
|
2024-12-12 |
|
f5c
|
public |
An optimised re-implementation of the call-methylation and eventalign modules in Nanopolish.
|
2024-12-12 |
|
hr2
|
public |
HR2 is a program to calculate elemental compositions for a given mass. This program and its documentation are Copyright (c) 1992-2005 by Joerg Hau
|
2024-12-12 |
|
segul
|
public |
An ultrafast and memory efficient tool for phylogenomics
|
2024-12-12 |
|
ucsc-mafspeciessubset
|
public |
Extract a maf that just has a subset of species.
|
2024-12-12 |
|
fastq-and-furious
|
public |
Fast handling of FASTQ files
|
2024-12-12 |
|
ucsc-hgloadnet
|
public |
Load a generic net file into database
|
2024-12-12 |
|
amplisim
|
public |
Plain simple amplicon sequence simulator for in-silico genomic sequencing assays.
|
2024-12-12 |
|
bed2gtf
|
public |
A high-performance BED-to-GTF converter written in Rust
|
2024-12-12 |
|
tantan
|
public |
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
|
2024-12-12 |
|
fgwas
|
public |
fgwas is a command line tool for integrating functional genomic information into a genome-wide association study (GWAS).
|
2024-12-12 |
