Questions tagged [taxonomy]
Use for questions involving the assignment of a taxonomic groups to each species, the ordering of species into categories of different hierarchical value, or the classification of organisms into species, genus, family, order, class and phylum.
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How to identify a bacterium species from its short RNA-seq transcriptomics data?
I am new to RNA-seq analysis and wanted to ask if there is a method to reliably identify the species of a microbial organism using only its raw short RNA transcriptomics data. Here are some of the ...
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short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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How many ML tree should I build?
I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood).
The choice of 20 iterations was based on a ...
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tBLASTn vs NCBI TSA
Is there a way to blast my proteins against all the TSA (Transcriptome Shotgun Assembly Sequence Database) belonging to a specific taxonomy using command line?
Thanks,
Marco
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MMSeqs taxonomy running for over a day
I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.
In their paper they claim ...
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getting NCBI TAXname by R
I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic
I believe one of the site members is an expert in Cyanobacteria hence the question.
I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__♦
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How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
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eggNOG API, how's it work?
Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
M__♦
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Parsing text within a taxonomy.csv file
I have the following file in tab separated values (TSV).
ID
Taxonomy
76980f6d906c6baaef3f96559fc7ba1b
d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured
...
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How can I download from NCBI all the ITS genes and the related taxonomy?
I would like to download all the ITS1 and ITS2 genes from NCBI in a fasta file. And, I'd like to download even the related taxonomy of each sequence.
Thanks,
Marco
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Assign multiple taxids to a sequence when constructing a local BLAST database
I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two ...
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Mapping NCBI taxID to divergence time?
I want to map NCBI taxID, specifically a pair of Genbank sequences, to the divergence time estimate of their common ancestor. For example, using a coalescence theory approach predominantly used in ...
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List of all Latin word parts used in Biological Taxonomy?
I seem to have determined that there are 287,614 unique Latin taxonomic names used in the biological taxonomy according to the Integrated Taxonomic Information System (ITIS) taxonomy taxon.txt file. ...
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Tool that can sort NCBI taxonomy ids based on phylogeny
I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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