15 votes
Accepted

How to convert species names into common names?

As Pierre mentioned, NCBI is a good resource for this kind of transformation. You can still use taxize to perform the conversion: ...
Iakov Davydov's user avatar
14 votes

How to convert species names into common names?

use the NCBI taxon dump under ftp://ftp.ncbi.nih.gov/pub/taxonomy in taxdmp.zip you'll find all the names for a given NCBI taxon ...
Pierre's user avatar
  • 1,536
7 votes
Accepted

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

No, there are no standardized three-letter abbreviations for species names. Three-letter abbreviations with roman letters is 26^3 combinations, which is only 17,576 possible combinations. As a result ...
conchoecia's user avatar
  • 3,161
6 votes

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

These are not. The closest to "standard" is the 5-character abbreviation by Swissprot. It names 25,886 species and has been used for decades. It is also easy to remember for some common species such ...
user172818's user avatar
  • 6,515
4 votes
Accepted

Software for taxonomic assignment?

You could take a look at kraken2 It should fit your purpose.
Mr_Z's user avatar
  • 629
4 votes

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

The NCBI taxonomy is a quite extensive resource: https://www.ncbi.nlm.nih.gov/taxonomy I would thus expect there is a good chance that it covers all of the taxa that you are interested in. It ...
jakebeal's user avatar
  • 653
4 votes

How to convert species names into common names?

Getting back to the original question about using taxize to search specifically in EOL, it looks like the most recent version of the package does not produce this ...
M.Whalen's user avatar
4 votes

Download complete Phylogenetic Tree as JSON

NCBI maintains an SQL dump of their taxonomic database You can see what that contains here For smaller requests (depending on what you need), you might also consider the ENSEMBL REST API - although I ...
Bastian Schiffthaler's user avatar
4 votes

How can I download from NCBI all the ITS genes and the related taxonomy?

I recommend to use Biopython: ...
Vovin's user avatar
  • 435
4 votes
Accepted

Assign multiple taxids to a sequence when constructing a local BLAST database

I inquired with the NCBI BLAST help desk today, and within an hour they provided a very helpful response. To summarize, when redundant records in the database are collapsed, the deflines (accessions + ...
Daniel Standage's user avatar
3 votes

How can I download from NCBI all the ITS genes and the related taxonomy?

For batch operations, it would be better to acquire a NCBI API key and combine GNU parallel and Entrez Direct . If you already have the accession numbers of ITS1 and ITS2 genes, put the accession ...
Forrest Vigor's user avatar
3 votes

Software for taxonomic assignment?

If you like blast, maybe you can try DIAMOND - the authors claim it's much faster than BLAST.
aLbAc's user avatar
  • 196
3 votes

Mapping NCBI taxID to divergence time?

I want to map NCBI taxID to their evolution time. Do we have a database for such correlation? It would be best to edit your question to clarify what you mean by "evolution time" since this ...
Daniel Standage's user avatar
3 votes
Accepted

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

If I understand correctly, your question boils down to: parsing a bunch of numbers in a row from a .csv file gives a different result from parsing a bunch of numbers as rows of a text file. I that ...
mdperry's user avatar
  • 258
2 votes
Accepted

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

Probably the best currently available online database is RBG Kew's Plants of the World Online. It organises taxonomic, morphological and distribution data from a range of databases. You can search for ...
NatWH's user avatar
  • 347
2 votes
Accepted

Demovir produces an empty output

maybe you can open the demovir.R file with Rstudio and execute line by line to check where the failure is. - @zorbax Thanks for your suggestion. I eventually got a correct final output already. The ...
Ernie Hsieh's user avatar
2 votes

Find species from FASTA files

Are you not allowed to use the web BLAST tool? That's what I use if I need to quickly find out the likely origin of a DNA sequence. There are command-line ways to do the same thing, but I only use ...
gringer's user avatar
  • 14.1k
2 votes
Accepted

Genetic relationships between Cyanobacteria: terrestrial vs aquatic

Ah! Finally, a question I can answer. There has been some pretty good work about this recently. In particular, I would reccomend this paper by Chen et al. , which groups cyanobacteria into terrestrial ...
Laura's user avatar
  • 909
2 votes

How many ML tree should I build?

Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker (several logs) and is strongly of identical performance to RAxML. ...
M__'s user avatar
  • 12.3k
1 vote

Parsing text within a taxonomy.csv file

The pandas solution is here: ...
M__'s user avatar
  • 12.3k
1 vote

Mapping NCBI taxID to divergence time?

Frontiers in Ecology and Evolution did a focused and succinct review looking at 'the Tree of Life' in 2017 here. They particularly highlight the importance of integrating a fossil record within ...
M__'s user avatar
  • 12.3k
1 vote

List of all Latin word parts used in Biological Taxonomy?

Maybe you can use NCBI Taxonomy instead, which is a full hierarchical taxonomy with >700K taxa. You can use Entrez utilities to programmatically query NCBI taxonomy to retrieve Latin or common ...
Chris_Rands's user avatar
  • 3,948
1 vote

Download complete Phylogenetic Tree as JSON

It would be worth looking at the Tree of Life web project, it isn't downloadable but its a reference source that can be improved on and updated in your website. ToL contains trees linking everything ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

Comparing groups of 16S rRNA sequences - how to?

If you want to make an all vs all with blast this can be helpful. You can create a blast database with your sequences and then search against itself. ...
zorbax's user avatar
  • 769
1 vote

Determine if an organism is microbic or unicellular

I would start by saying that your statement that no animals/plants are microbes is false. There are indeed microbial algae (plants) and microbial animals. So it is indeed difficult. (I'll briefly ...
Maximilian Press's user avatar
1 vote

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

I am not NGS expert, I known ML. Essentially you are performing data augmentation which is essential for ML. What I question is whether a replicate of e6 from a population of e7 would really be ...
M__'s user avatar
  • 12.3k
1 vote

Python module for fetching NCBI id for a list of species

This isn't a Python library, but it's easily invoked from Python code, easy to install, and has a lot of useful features. I just discovered the amazing taxonkit library this week. In particular, the <...
Daniel Standage's user avatar
1 vote

Python module for fetching NCBI id for a list of species

Biopython has an efetch frontend. ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

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

I overlooked the fact that (for my data) about 1:50,000 results returned from my blasting yielded a ";" within the hit denoting two taxids and did not account for these in my script. How a given ...
ljs's user avatar
  • 265
1 vote

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

The maximum number of steps (or changes) is the number of taxa with state 1 or 0, whichever is smaller. Conceptually, this is the number of character changes if each taxon evolved its state ...
Kohl Kinning's user avatar
  • 1,149

Only top scored, non community-wiki answers of a minimum length are eligible