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I am currently interested in algae taxonomy (I am not an expert in the field).

I retrieved the taxonomy of my sequences with their NCBI access number via the taxonkit software (https://bioinf.shenwei.me/taxonkit/usage/).

I noticed that I get Cryptophyta at the Class rank level.

For me -phyta actually corresponds more to the phylum rank.

I checked on NCBI site and is actually tidy in Class rank ( https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3027&lvl=3&lin=f&keep=1&srchmode=1&unlock) but for example on the algaebase database (http://www.algaebase.org/browse/taxonomy/detail/?taxonid=Xafa8c1d30aa53593), Cryptophyta is classified as Phylum.

Can you tell me why Cryptophyta is rank at the Class level on NCBI and not to the Phylum level ?

Conversely, I retrieve taxonomy with, for example, Phaeophyceae ranked at Phylum level (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2870&lvl=3&lin=f&keep=1&srchmode= 1 & unlock) while it is normally a Class on algaebase (http://www.algaebase.org/browse/taxonomy/detail/?taxonid=L8055ac0a94735f3e).

Do you have ideas being considered? I am very interested !

Thank you very much in advance for your answers.

Best regards

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It is not possible to tell which one is "correct" and which one is "incorrect"; Actually "ranking" itself is a bigger problem with entire classification system.

After the "sexual species concept" we have somewhat a grasp that many (but not all) species fall on "same rank"; but for supra-specific ranks it is theoretically impossible to tell whether the grass (said to be "family" rank) and a compositae (said to be "family" rank) fall exactly on same "rank" or not; similarly it is theoretically impossible to tell whether the animal (said to be kingdom rank) and plants (said to be kingdom rank) are exactly on same rank.

Practically; we forcefully assign the taxa from different lineages into similar ranks somewhat based on apparent perception, and in some cases we develop fine divisions of ranks and develop some criteria, that is also based on perception of 1 or a team op people; but that is not absolute.

What we can theoretically confirm, the taxon "Plant" is certainly higher than (superset of) the taxon "grass" (a subset). I.e. hierarchies (superset-subset relationship) exist along a lineage. But the concept of "rank"; i.e. assigning 2 taxa from different lineage into "ranks" is a highly subjective and controversial. (Personally I confess I don't know whether the ranking system have any real advantage other than arranging information)

A routine change of rank usually does not make anything correct or incorrect. (if within the single lineage you assigned a phylum into order and simultaneously an order into phylum; then it would be a clear false, or jumble-up the subset-superset relation). But when you just change a vague and confusing sort of "weightage" with respect to taxa on other lineages; keeping all subset-superset relations unaltered; nothing actually changes!

N.B. Additionally, if a taxon (set) is broken into adjacent or more taxa, or 2 adjacent taxa (set) is fused, (without cutting a taxon from one lineage to another) that is also a minor change in "refinement" or "resolution", not a change in correct-or-incorrect-ness.

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    $\begingroup$ Thank you very much for your detailed answer but would you have some thoughts on Cryptophyta? $\endgroup$ – Tof Aug 9 '18 at 20:44
  • $\begingroup$ Thanks for letting me know a question. I'll update the answer as soon I'll be free to write. $\endgroup$ – Always Confused Aug 18 '18 at 16:43

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