Streamlining phylogenomic data gathering, processing and visualization
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Updated
Sep 26, 2018 - Python
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orthologues
Here are 8 public repositories matching this topic...
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
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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Apr 21, 2024 - Perl
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
python
shell
bash
data-science
bioinformatics
genetics
biology
ftp
sge
phylogenetics
blast
orthologues
qsub
orthology-inference
ncbi
sequence-alignment
pbs
orthologs
orthology
biosql
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Updated
May 7, 2024 - Python
A couple of tools I find indispensable for post orthomcl down-stream analysis.
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Oct 2, 2019 - Perl
Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".
science
data-science
bioinformatics
pipeline
genetics
ngs
bioinformatics-pipeline
phylogenetics
data-analysis
orthologues
phylogenomic
transcriptome
phylogenomics
molecular-biology
bioinformatics-analysis
ngs-analysis
taxonomic-classification
phylogenomics-pipeline
ngs-pipeline
hybseq-data
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Updated
Feb 16, 2024 - TeX
Find two-boxes transcription factor binding sites (made for sigma factor binding sites) by comparing intergenic DNA regions upstream pairs of orthologous genes using statistical analyses
statistics
prediction
orthologues
promoter
transcription-factor-binding-site
sigma-factor-binding-site
dna-motifs
rmes
sigffrid
bmc-bioinformatics
two-box-motifs
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Oct 6, 2020 - Perl
Phylogenetic tree of LAR and other PIP family enzymes as shown in Güngör et al. 2020. This repository details all code and intermediate files used.
biology
open-data
open-science
orthologues
phylogeny
science-research
protein-evolution
open-notebook
plant-genetic-resources
plant-genomics
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Oct 6, 2020 - Jupyter Notebook
The local version of the RecBlast
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Updated
Mar 4, 2017 - Python
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