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fasttree
|
public |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
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2023-06-16 |
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phyml
|
public |
Phylogenetic estimation using (Maximum) Likelihood
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2023-06-16 |
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umi_tools
|
public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
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2023-06-16 |
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amas
|
public |
Calculate various summary statistics on a multiple sequence alignment
|
2023-06-16 |
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raxml-ng
|
public |
RAxML Next Generation: faster, easier-to-use and more flexible
|
2023-06-16 |
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tectonic
|
public |
A modernized, complete, standalone TeX/LaTeX engine.
|
2023-06-16 |
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rust
|
public |
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
This package provides the compiler (rustc) and the documentation utilities rustdoc.
|
2023-06-16 |
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biopython
|
public |
Freely available tools for computational molecular biology.
|
2023-06-16 |
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bioconductor-ggtree
|
public |
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
|
2023-06-16 |
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htmlmin
|
public |
An HTML Minifier
|
2023-06-16 |
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sierralocal
|
public |
Local execution of HIVdb algorithm
|
2023-06-16 |
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dendropy
|
public |
A Python library for phylogenetics and phylogenetic computing
|
2023-06-16 |
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tn93
|
public |
fast pairwise Tamura Nei 93 distance calculator
|
2023-06-16 |
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hyphy-helper
|
public |
An intuitive HyPhy interface for Python
|
2023-06-16 |
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hyphy-python
|
public |
HyPhy package interface library
|
2023-06-16 |
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hivclustering
|
public |
A Python 3 library that makes inferences on HIV-1 transmission networks
|
2023-06-16 |
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fakemp
|
public |
Fake multiprocessing pool objects
|
2023-06-16 |
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hivtrace
|
public |
Reconstruction and analysis of HIV-1 molecular transmission networks
|
2023-06-16 |
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bioext
|
public |
A few handy bioinformatics tools not already within BioPython
|
2023-06-16 |
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fuzzywuzzy
|
public |
Fuzzy string matching in python
|
2023-06-16 |
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python-levenshtein
|
public |
Python extension for computing string edit distances and similarities
|
2023-06-16 |
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rx
|
public |
Reactive Extensions (Rx) for Python
|
2023-06-16 |
|
sierrapy
|
public |
A Client of HIVdb Sierra GraphQL Webservice
|
2023-06-16 |
|
promise
|
public |
Promises/A+ implementation for Python
|
2023-06-16 |
|
graphql-core
|
public |
GraphQL implementation for Python
|
2023-06-16 |
|
syn-scan
|
public |
Synonymous Nonsynonymous Mutation Rates between Sequences Containing Ambiguous Nucleotides
|
2023-06-16 |
|
gql
|
public |
GraphQL client for Python
|
2023-06-16 |
|
voluptuous
|
public |
Voluptuous is a Python data validation library
|
2023-06-16 |
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iqtree
|
public |
Efficient phylogenomic software by maximum likelihood
|
2023-06-16 |
|
blastn
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit
|
2023-06-16 |
|
quasitools
|
public |
Quasitools is a collection of tools for analysing Viral Quasispecies
|
2023-06-16 |
|
ampliconclipper
|
public |
An alignment postprocessor that removes PCR primers from SAM alignments and discards reads with major errors
|
2023-06-16 |
|
blastdb
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit
|
2023-06-16 |
|
scons
|
public |
Open Source next-generation build tool.
|
2023-06-16 |
|
fastaq
|
public |
Python3 scripts to manipulate FASTA and FASTQ files
|
2023-06-16 |
|
pear
|
public |
PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger
|
2023-06-16 |
|
pysam
|
public |
Python module for reading and manipulating SAM/BAM/VCF/BCF files
|
2023-06-16 |
|
bambamc
|
public |
lightweight C implementation of name collating BAM file input and BAM file output
|
2023-06-16 |
|
fastx_toolkit
|
public |
FASTA/FASTQ pre-processing programs
|
2023-06-16 |
|
picard
|
public |
Java tools for working with NGS data in the BAM format
|
2023-06-16 |
|
prinseq
|
public |
PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data
|
2023-06-16 |
|
matplotlib
|
public |
Publication quality figures in Python
|
2023-06-16 |
|
mafft
|
public |
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
|
2023-06-16 |
|
hivmmer
|
public |
An alignment and variant-calling pipeline for Illumina deep sequencing of HIV-1, based on the probabilistic aligner HMMER.
|
2023-06-16 |
|
iva
|
public |
de novo virus assembler of Illumina paired reads
|
2023-06-16 |
|
bowtie2
|
public |
Fast and sensitive read alignment
|
2023-06-16 |
|
samtools
|
public |
Tools for dealing with SAM, BAM and CRAM files
|
2023-06-16 |
|
trimmomatic
|
public |
A flexible read trimming tool for Illumina NGS data
|
2023-06-16 |
|
hmmer
|
public |
Biosequence analysis using profile hidden Markov models
|
2023-06-16 |
|
smalt
|
public |
SMALT aligns DNA sequencing reads with a reference genome.
|
2023-06-16 |
