Hi Zili Yuan,

First thing, you need to blast your sequences on one of the genebanks to get similar sequences to yours. I recommend the NCBI website (https://www.ncbi.nlm.nih.gov/). It`s easy to use and you can download similar sequences easily. after that, you need to use phylogenetic analysis software. I personally use MEGAX but you can use R if you wish.

I hope this answer brought you some help.

Good luck

You can use entrez-direct from ncbi (under linux) in while loop :

cat mylist | while read line

do echo -e $line >> count.txt

esearch -db nucleotide -query "$line[ORGN]" | grep "^ " >> count.txt; done

-mylist is your list of 23k plant species, one species "genus species" per line

-this script will create a file "count.txt in which for each species you find a number indicating the count of nuclletoide records found in ncbi.

good luck

You can download the sequences from the NCBI, and for phylogenetic analysis, you can use MEGA or R software

I hope this answer helps