phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes (by biobakery)
biobakery_workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. (by biobakery)
| phylophlan | biobakery_workflows | |
|---|---|---|
| 1 | 1 | |
| 135 | 110 | |
| 2.2% | 3.6% | |
| 6.5 | 4.6 | |
| 3 months ago | 2 months ago | |
| Python | Python | |
| MIT License | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
phylophlan
Posts with mentions or reviews of phylophlan.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-02-16.
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PhyloPhlAN Tutorial?
I am trying to use PhyloPhlAn (https://github.com/biobakery/phylophlan). I have read the wiki in GitHub it is very confusing. I tried several runs but it came out as an error.
biobakery_workflows
Posts with mentions or reviews of biobakery_workflows.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-12-29.
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Any good meta-transcriptomics pipelines
The bio bakery has some meta-transcriptomic pipelines on it. They also maintain the mertaphlan and humann packages that are almost becoming the defacto standard when analysing shot gun reads. https://github.com/biobakery/biobakery_workflows
What are some alternatives?
When comparing phylophlan and biobakery_workflows you can also consider the following projects:
pyCircos - python Circos
sourmash - Quickly search, compare, and analyze genomic and metagenomic data sets.
graphlan - High-quality circular representations of taxonomic and phylogenetic trees
GEMAP_NCLDV - Genome Mapping Analysis Pipeline for giant viruses
empress - A fast and scalable phylogenetic tree viewer for microbiome data analysis
dndserver - Dark and Darker private server implementation written in Python