Hello, everyone,
One of the aims of my current study is to place a particular plant species within the context of the whole genus phylogenetically. The systematic position of these plant species is well known. But the species that I have in hand is rare and endemic and its phylogenetic position is obscured.
I will launch a phylogenetic analysis of the DNA sequences of this plant species. I have a few DNA sequences of 5 markers. Please I need help and answers to the following points:
1- I did a BLASTn search, should I use Mega blast search instead?
2- If the retrieved list includes a plant species with several accessions, should I download all accessions or just one accession for each species is enough for the phylogenetic analysis?
3- What is the threshold of similarity percent to the query sequence I should select?
4- How many accessions needed to cover the diversity of the plant species under investigation?
5- Which phylogenetic analysis methodology suits systematic research, (i.e.) Bayesian analysis, Maximum likelihood, or something else?
1- Any homology search tool should be fine, yes it's better to use megablast and even better to use protein sequences than nucleotide sequences in this case i recommend to use DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST).
2- Generally more representative sequences more robust tree you got. Also, more balance group-sequences representatives are recommended.
3- there is no similarity cut off but it's better to go for 90% and more similarity. keeping the sequence coverage in mind.
4- i think this point was covered is #2
5- Both Bayesian analysis and Maximum likelihood is recommended.
Do the MAT K/ ITS2 region (for barcoding genes) analysis. BLAST should be enough for phylogenetic tree neighbor joining method should be ok enough. Go for the least E values to select entries from BLAST results and similarity score is basically. "Higher the similarity score better the entry is"
- Badges
- Science method