[ 原始碼： gubbins ]
套件：gubbins（3.4-1）
phylogenetic analysis of genome sequences
Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
其他與 gubbins 有關的套件
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- dep: libc6 (>= 2.34)
- 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
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-biopython
- Python3 library for bioinformatics
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- dep: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)
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- dep: python3-multiprocess
- better multiprocessing and multithreading in Python
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- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
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- dep: python3-scipy
- scientific tools for Python 3
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- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
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- dep: zlib1g (>= 1:1.1.4)
- 壓縮函式庫 - 跑程式時用(runtime)
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- rec: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- rec: iqtree
- efficient phylogenetic software by maximum likelihood
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- sug: r-base-core
- GNU R core of statistical computation and graphics system