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Package Name Access Summary Updated
r-goalie public Assertive check functions for defensive R programming. 2024-12-12
cofold public An RNA secondary structure prediction method that takes co-transcriptional folding into account. 2024-12-12
nmrglue public A module for working with NMR data in Python 2024-12-12
maxit public MAXIT assists in the processing and curation of macromolecular structure data. 2024-12-12
abpoa public abPOA: fast SIMD-based partial order alignment using adaptive band 2024-12-12
trf public Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. 2024-12-12
ucsc-countchars public Count the number of occurrences of a particular char 2024-12-12
vcftools public A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries 2024-12-12
seqtk public Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format 2024-12-12
ninja-nj public Nearly Infinite Neighbor Joining Application 2024-12-12
scssim public A bioinformatics tool for simulating single-cell genome sequencing data 2024-12-12
ucsc-wordline public chop up words by white space and output them with one 2024-12-12
sdust public Symmetric DUST for finding low-complexity regions in DNA sequences. 2024-12-12
haploflow public Strain-aware viral genome assembler for short read sequence data 2024-12-12
mapcaller public MapCaller: combined short-read mapper and variant caller 2024-12-12
ucsc-netsplit public Split a genome net file into chromosome net files 2024-12-12
ucsc-qacagplift public Use AGP to combine per-scaffold qac into per-chrom qac. 2024-12-12
mergenotcombined public Merge Forward and reverse reads from fastq files 2024-12-12
bamhash public No Summary 2024-12-12
ucsc-faalign public Align two fasta files 2024-12-12
evidencemodeler public Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures 2024-12-12
booster public BOOSTER is a new way of computing bootstrap supports in large phylogenies. 2024-12-12
rustynuc public Quick analysis of pileups for likely 8-oxoG locations 2024-12-12
assemblyutility public No Summary 2024-12-12
smoothxg public Local reconstruction of variation graphs using partial order alignment 2024-12-12
vcfbub public Popping bubbles in vg deconstruct VCFs 2024-12-12
ucsc-pslsortacc public Remove chain-breaking alignments from chains that break nested chains. 2024-12-12
python-hyphy-python public HyPhy package interface library 2024-12-12
fastsimbac public Models bacterial recombination 2024-12-12
selam public Simulation of Epistasis Local adaptation, with Ancestry and Mate choice 2024-12-12
ucsc-catdir public concatenate files in directory to stdout. 2024-12-12
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
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

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