Parents (Total: 1380)

The searched file hash is included in 1380 parent files which include package known and seen by metalookup. A sample is included below:

Key	Value
FileSize	2927684
MD5	D71DEDD21E01E854442C929A2C4A89B9
PackageDescription	quality filtering tool for long reads of genome sequences Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	filtlong
PackageSection	science
PackageVersion	0.2.0-2
SHA-1	000A26FE05A6F212B109B0AE8BFFF64D08E9012B
SHA-256	6CA1E88A62870C08E482A31AA1C48295232063503401735FF1D5E012E46AE876

Key	Value
FileSize	2624844
MD5	7DC1B75421C4DA84E958F89BE63B67FF
PackageDescription	efficient phylogenetic software by maximum likelihood IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others: . * A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015) * An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013). * A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments. * Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest. * Finding best partition scheme like PartitionFinder. * Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes. * Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014)
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	iqtree
PackageSection	science
PackageVersion	1.6.9+dfsg-1
SHA-1	0027785DDEB4CA9C4315398E3B22D5D10D40B2B7
SHA-256	228C7979A6A69881A4134DEBF2F24D15051D997BE45F67766F8933EB431454B4

Key	Value
FileSize	690368
MD5	4F0AE959248C522A7FDEF5A813ECE026
PackageDescription	structural variation caller using third-generation sequencing Sniffles is a structural variation (SV) caller using third-generation sequencing data such as those from Pacific Biosciences or Oxford Nanopore platforms. It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	sniffles
PackageSection	science
PackageVersion	1.0.12b+ds-1
SHA-1	003ABC1C1FF195F62782435BBE5CFE02C613F174
SHA-256	7558383502011E4D7B66FD17043F58C8FCACB698DCC1982B4CBB8AD81D4D3333

Key	Value
FileSize	178104
MD5	B28B945615CD8EF86C84DD28BD446892
PackageDescription	manage nucleotide sequencing read data To facilitate the multiple phases of the dazzler assembler, all the read data is organized into what is effectively a database of the reads and their meta-information. The design goals for this data base are as follows: * The database stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files. This avoids duplicating the same data, once in the source file and once in the database. * The data base can be built up incrementally, that is new sequence data can be added to the data base over time. * The data base flexibly allows one to store any meta-data desired for reads. This is accomplished with the concept of *tracks* that implementors can add as they need them. * The data is held in a compressed form equivalent to the .dexta and .dexqv files of the data extraction module. Both the .fasta and .quiva information for each read is held in the data base and can be recreated from it. The .quiva information can be added separately and later on if desired. * To facilitate job parallel, cluster operation of the phases of the assembler, the database has a concept of a *current partitioning* in which all the reads that are over a given length and optionally unique to a well, are divided up into *blocks* containing roughly a given number of bases, except possibly the last block which may have a short count. Often programs can be run on blocks or pairs of blocks and each such job is reasonably well balanced as the blocks are all the same size. One must be careful about changing the partition during an assembly as doing so can void the structural validity of any interim block-based results.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	dazzdb
PackageSection	science
PackageVersion	1.0+git20201103.8d98c37-1+deb11u1
SHA-1	003C12AE2FCDE5DDDC4601D5CB4B875E9E3C710A
SHA-256	90C08948CDA010BC55E5D894E8BC292C8C60AF376242FB5C14FBF6E88134FD1D

Key	Value
FileSize	13192
MD5	22B9D8FC434C1BCD6BB0C5063C08B4A9
PackageDescription	determine similar regions between two strings or genomic sequences The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings or nucleotide or protein sequences. Instead of looking at the total sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	smithwaterman
PackageSection	science
PackageVersion	0.0+git20160702.2610e25-11
SHA-1	0040B5563DFDC347FECCF2374AB27FEF11705B15
SHA-256	D483E0677FD2F17B6BFF5C672A4D85E35EE97F567B82C02643138762D926BA34

Key	Value
FileSize	23808
MD5	D3F18FE81CC30757847FCF0C416F41A0
PackageDescription	coiled coil secondary structure prediction The program predicts the coiled coil secondary structure predictions from protein sequences. The algorithm was published in Lupas, van Dyke & Stock, Predicting coiled coils from protein sequences Science, 252, 1162-1164, 1991.
PackageMaintainer	Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
PackageName	ncoils
PackageSection	science
PackageVersion	2002-7
SHA-1	009BE594705498ACA3B41A71C301DC728230BB15
SHA-256	035609DEBC7DD786FFC3C96F685DECFAE78E130C212A68912950E53698C1FD1D

Key	Value
FileSize	179892
MD5	8913B920C6C4B80AABB65BDFDDBD159B
PackageDescription	Wisconsin's High-Throughput Alignment Method This package provides functionality analogous to BWA or bowtie in aligning reads from next-generation DNA sequencing machines against a reference genome.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	wham-align
PackageSection	science
PackageVersion	0.1.5-8
SHA-1	009FCE939CB65630C746B6D0D4D50E17DFB4FBAC
SHA-256	D6A15B500E86173F14B399D0CD2A9300AFB50CEDD267E80F08DA0B762E30FB5E

Key	Value
FileSize	1173252
MD5	8243AB32CDB2B301F861D1D53BE24F28
PackageDescription	Functions for Base Types and Core R and 'Tidyverse' Features A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
PackageMaintainer	Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
PackageName	r-cran-rlang
PackageSection	gnu-r
PackageVersion	0.4.11-1
SHA-1	00B23F2F72110750848556BEC3A08FEF47DA8AF4
SHA-256	B5BDEE91D0D41CA761A82C1951C343E0FB8F533798E4C27610BEE2A80965BFA7

Key	Value
FileSize	192928
MD5	00364D492927E73E8A724E013C52B39A
PackageDescription	rapid core genome multi-alignment Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
PackageMaintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
PackageName	parsnp
PackageSection	science
PackageVersion	1.5.6+dfsg-1
SHA-1	00CCDA7EEB6573E0959EF2480B6EE248AF2E93B7
SHA-256	AACE429538C543EFD1B3C1D8E36A8F512D12C44F30B4A22268A45AB4DCF347C6

Key	Value
FileSize	94476
MD5	2D2F28A88FDB08E2C5C903DDF97B32AC
PackageDescription	engine for running and embedding Groovy in a Java virtual machine Grengine allows one to run Groovy code in a Java VM, in a way that is quick, highly configurable and thread-safe. When the default behavior does not suit the users' needs, classes can be overridden to change the way the framework behaves. Even without writing new classes, there are ways to configure the engine quite a lot.
PackageMaintainer	Debian Java Maintainers <pkg-java-maintainers@lists.alioth.debian.org>
PackageName	libgrengine-java
PackageSection	java
PackageVersion	3.0.0+dfsg-2
SHA-1	00D7B7AB2A7CF19E8AF94F9BA76AFA547AA26DD6
SHA-256	3FFA7840D09E9AB5249699B306F60A5627742AFCF7D3A86F6235C8705F6DF886