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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 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 ...
Mirko's user avatar
  • 267
0 votes
1 answer
37 views

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
Marco's user avatar
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1 vote
1 answer
45 views

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 ...
Rainman's user avatar
  • 171
0 votes
1 answer
30 views

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 ...
Farzad Beikpour's user avatar
1 vote
1 answer
90 views

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__'s user avatar
  • 12.5k
1 vote
1 answer
283 views

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 '...
K_081's user avatar
  • 149
1 vote
0 answers
57 views

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__'s user avatar
  • 12.5k
2 votes
1 answer
97 views

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 ...
Marco's user avatar
  • 161
3 votes
2 answers
253 views

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
Marco's user avatar
  • 161
4 votes
1 answer
398 views

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 ...
Daniel Standage's user avatar
1 vote
2 answers
47 views

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 ...
Johnny Tam's user avatar
1 vote
1 answer
142 views

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. ...
Lance's user avatar
  • 143
1 vote
0 answers
47 views

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 ...
snord's user avatar
  • 11
2 votes
1 answer
58 views

Demovir produces an empty output

I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs. First, I installed all ...
Ernie Hsieh's user avatar
1 vote
1 answer
329 views

Find species from FASTA files

In a school project we got the task of finding the species from two FASTA files. We got some hints of what to look for, like it is a unicellular eukaryote and that we can use blast. We don't know if ...
ingrle's user avatar
  • 21
2 votes
2 answers
1k views

Download complete Phylogenetic Tree as JSON

I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this: ...
Tom's user avatar
  • 121
0 votes
1 answer
29 views

Comparing groups of 16S rRNA sequences - how to?

I have several groups of 16S rRNA sequences associated with taxonomic groups (let's call them A, B and C). The sequences within each group have a common ancestor and are on average more closely ...
Laura's user avatar
  • 927
2 votes
2 answers
65 views

Software for taxonomic assignment?

I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable ...
Laura's user avatar
  • 927
4 votes
0 answers
1k views

Kraken2 > OTU format > Phyloseq

A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to make a tree if the data using a ...
Reebola95's user avatar
1 vote
0 answers
34 views

Generating taxonomic hierarchy by species/genus name

I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
uvnomad's user avatar
  • 21
0 votes
1 answer
38 views

Determine if an organism is microbic or unicellular

I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup. For this, it would be useful to be able to distinguish whether a specific organism is a ...
Wrzlprmft's user avatar
  • 101
1 vote
0 answers
77 views

Analyzing a blast result of NGS data

I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI. I filtered those read data whose paired ends ...
Adrián P.L.'s user avatar
4 votes
1 answer
680 views

What is a proper way for random subsampling of metagenomic data?

Let's say we have a metagenomic sample that is paired-end FASTQ files including 10,000,000 DNA reads collected using shotgun sequencing. How would one make a random subsample of the mentioned ...
Remy's user avatar
  • 53
2 votes
1 answer
57 views

Which taxonomy data type to use for abundance graphs and statistical analyses?

At our institution we have had some debate about this topic. So let me give some background: Qiime2 produces a OTU table which shows the number of sequences that matched to a specific OTU. It also ...
Roelof Coertze's user avatar
1 vote
3 answers
714 views

Python module for fetching NCBI id for a list of species

I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
Ahmed Abdullah's user avatar
2 votes
0 answers
145 views

How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
Ahmed Abdullah's user avatar
2 votes
2 answers
137 views

Looking for a taxonomic dataset that links tree genera (or species) to families

I am looking for a taxonomic dataset that would allow me to links tree genera (or species) to families. In particular, I am interested in the tropical species found in the Amazon. I found a long but ...
Davide Leonessi's user avatar
2 votes
1 answer
585 views

Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"

I am using this script: ...
ljs's user avatar
  • 265
4 votes
1 answer
1k views

In calculating the retention index, why do we use the character state with the lowest frequency?

To calculate the retention index for a phylogenetic tree, we use the following formula: $$\frac{\text{maximum number of steps on tree - number of steps on the tree}} {\text{maximum number of steps on ...
Namenlos's user avatar
  • 317
8 votes
2 answers
680 views

Are these standard species abbreviations and how to look up others?

Reactome uses a three letter code for each species which are listed below. Are the letter codes used by Reactome a standard? If so is there a web page or download file that can validate the code and ...
Guy Coder's user avatar
  • 315
8 votes
1 answer
689 views

Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields "400 Bad Request" error?

I've been searching TaxIDs against NCBI's Taxonomy DB to get taxonomic lineages for species. I have successfully done this for 1,000's of TaxIDs that were returned to me by Blast+ blasts in a CSV. (...
ljs's user avatar
  • 265
2 votes
1 answer
40 views

What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?

I want to read out the taxonomy id of the source organism of a pdb entry using the xml-file of the entry that is provided under ...
C. Zeil's user avatar
  • 23
5 votes
2 answers
321 views

Microbial diversity analysis using whole-genome metagenomic data

I have data, obtained from a single metagenomic DNA sample, that consists of two MiSeq FASTQ files (R1 and R2) that I merged using PEAR. Now I want to estimate the abundances of the bacteria taxa to ...
elsoja's user avatar
  • 241
11 votes
5 answers
4k views

How to convert species names into common names?

I’m trying to find common names from a list of scientific names (not all will have them though). I was attempting to use taxize in R but it aborts if it doesn’t ...
Daniel Mead's user avatar