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r-ape
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public |
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
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2025-03-25 |
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python-edlib
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public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
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2025-03-25 |
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muscle
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public |
MUSCLE: multiple sequence alignment with high accuracy and high throughput
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2025-03-25 |
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parasail-python
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public |
Python bindings for the parasail C library containing implementations of pairwise sequence alignment algorithms.
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2025-03-25 |
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racon
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public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
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2025-03-25 |
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miniasm
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public |
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
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2025-03-25 |
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mafft
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public |
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
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2025-03-25 |
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bwa
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public |
The BWA read mapper.
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2025-03-25 |
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spoa
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public |
SIMD partial order alignment tool/library
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2025-03-25 |
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mash
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public |
Fast sequence distance estimator that uses MinHash
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2025-03-25 |
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capnproto
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public |
An insanely fast data interchange format and capability-based RPC system.
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2025-03-25 |
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trnascan-se
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public |
tRNA detection in large-scale genomic sequences
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2025-03-25 |
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infernal
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public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
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2025-03-25 |
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diamond
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public |
Accelerated BLAST compatible local sequence aligner
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2025-03-25 |
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blast
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public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
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2025-03-25 |
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pychopper
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public |
A tool to identify, orient and rescue full length cDNA reads from nanopore data.
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2025-03-25 |
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rasusa
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public |
Randomly subsample sequencing reads to a specified coverage
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2025-03-25 |
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mbtools
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public |
mbtools - toolkit for working with modification BAM files
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2025-03-25 |
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mappy
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public |
Minimap2 Python binding
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2025-03-25 |
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pore-c-py
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public |
Python scripts for working with Pore-C data
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2025-03-25 |
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entrez-direct
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public |
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
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2025-03-25 |
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taxonkit
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public |
A Cross-platform and Efficient NCBI Taxonomy Toolkit
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2025-03-25 |
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bracken
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public |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
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2025-03-25 |
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bedtools
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public |
A powerful toolset for genome arithmetic
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2025-03-25 |
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kraken2
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public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2025-03-25 |
