#
phylogenetics
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Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
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Jul 23, 2021 - Python
RAxML Next Generation: faster, easier-to-use and more flexible
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Jul 27, 2021 - C++
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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Jul 15, 2021 - Python
Bayesian Evolutionary Analysis by Sampling Trees
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Jul 30, 2021 - Java
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
snps
binary
nexus
vcf
phylogenetics
alignment
fasta
snapp
phylip
vcf-files
polyploid
haploid
phylogenetic-analysis
outgroup
convert-snps
vcf-format
phylip-matrix
diploid
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Mar 18, 2021 - Python
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
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Jul 9, 2021 - C
HyPhy: Hypothesis testing using Phylogenies
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Jul 23, 2021 - HyPhy
Efficient phylogenomic software by maximum likelihood
phylogenetics
model-selection
mixture-model
maximum-likelihood
phylogenomics
iq-tree
ultrafast-bootstrap
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Apr 20, 2021 - C++
Bayesian Evolutionary Analysis Sampling Trees
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Jul 28, 2021 - Java
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
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Jul 28, 2021 - C
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
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Jul 16, 2021 - Python
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
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Aug 18, 2019 - Python
phylogenetics tools for linux (and other mostly posix compliant) computers
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Jul 10, 2021 - C++
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
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Apr 7, 2021 - C++
Streamlining phylogenomic data gathering, processing and visualization
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Sep 26, 2018 - Python
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mufernando
commented
Jun 23, 2021
this would be simple, as watterson's theta is
ts.segregating_sites()/sum([1/i for i in range(1, ts.num_samples])
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
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Mar 30, 2021 - Python
Pandas DataFrames for phylogenetics
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Jun 6, 2021 - Python
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
bioinformatics
bioinformatics-pipeline
phylogenetics
orthology
homology
ncbi-sra
gene-sequence-retrieval
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Apr 2, 2021 - Python
Massively parallel phylogenetic placement of genetic sequences
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Mar 26, 2021 - C++
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics
genomics
phylogenetic-trees
phylogenetics
epidemiology
network-visualization
hiv
cdc
phylogenomics
phylogeny
sequence-alignment
genomic-data-analysis
genomics-visualization
pathogens
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Jul 26, 2021 - HTML
A library for working with phylogenetic and population genetic data.
c-plus-plus
phylogenetic-trees
phylogenetics
population-genetics
evolutionary-placement
phylogenetic-data
placement
pool-sequencing
phylogenetic-placements
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Jul 9, 2021 - C++
Version 5 of the CAFE phylogenetics software
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Apr 30, 2021 - C++
A toolkit for analyzing and visualizing phylogenetic (placement) data
c-plus-plus
phylogenetics
genesis
evolutionary-placement
phylogenetic-data
placement
phylogenetic-placement
gappa
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May 10, 2021 - C++
Ultrafast Sample Placement on Existing Trees
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Jul 30, 2021 - C++
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
visualization
ruby
java
genomics
biology
evolution
computational-biology
phylogenetic-trees
phylogenetics
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Jul 26, 2021 - Java
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
docker
modular
virus
simulation
evolution
transmission
phylogenetics
robust
hiv
evolution-simulator
transmission-network
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Jul 23, 2021 - Python
A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy
bash
r
pipeline
genomics
perl
phylogenetic-trees
phylogenetics
markers
orthologues
microbiology
population-genetics
codon-alignment
maximum-likelihood
phylogenomics
species-trees
recombination
core-genome
species-delimitation
phylogenomics-pipeline
clock-hypothesis
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Jan 31, 2021 - Perl
babette is an R package to work with BEAST2
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Jul 24, 2021 - R
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Is there a schedule to add the deprecation warning as per:
https://github.com/biopython/biopython/blob/870f623005ed1b95df877f618cbb12a815bd5696/Bio/SeqFeature.py#L158-L175