[ 原始碼： parsnp ]
套件：parsnp（2.0.6+dfsg-1）
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.
其他與 parsnp 有關的套件
|
|
|
|
-
- dep: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
-
- dep: harvest-tools
- archiving and postprocessing for reference-compressed genomic multi-alignments
-
- dep: libc6 (>= 2.38)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
-
- dep: libgcc-s1 (>= 3.5)
- GCC 支援函式庫
-
- dep: libgomp1 (>= 6)
- GCC OpenMP (GOMP) support library
-
- dep: libmuscle1 (>= 3.7+4565)
- multiple alignment library for protein sequences
-
- dep: libstdc++6 (>= 14)
- GNU Standard C++ Library v3
-
- dep: mummer
- Efficient sequence alignment of full genomes
-
- dep: phipack
- PHI test and other tests of recombination
-
- dep: python3
- interactive high-level object-oriented language (default python3 version)
-
- dep: python3-biopython
- Python3 library for bioinformatics
-
- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
-
- dep: python3-pyspoa
- Python bindings to spoa
-
- dep: python3-tqdm
- fast, extensible progress bar for Python 3 and CLI tool
-
- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
-
- dep: time
- GNU time program for measuring CPU resource usage
-
- rec: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)