I want to construct a phylogenetic tree using almost 2000 sequences from prokaryotes as well as eukaryotes. To simply the tree, I would like to shortlist the sequences. What is the best way forward to do it without any bias in selecting the sequences?
First, are your sequences nucleotide or protein sequences? if they are nucleotide sequences then, and since you are including eukaryotes, you should take care of possible introns within the eukaryotic sequences.
Second, what gene your sequences encode? is it a protein-coding gene or not? well, depending on this you might probably want to cluster your sequences at an appropriate sequence similarity (or identity) value, and then select only a representative of each resulting cluster. However, it is not clear how to define an identity threshold to do this for any gene sequence and even more problematic can be when you are mixing prokaryotic and eukaryotic sequences. For clustering tools you might want to take a look at this question here in RG:
https://www.researchgate.net/post/Clustering_BLAST_search_results_by_species
That is all I can recommend with the information that you have provided.
Best regards.
First, are your sequences nucleotide or protein sequences? if they are nucleotide sequences then, and since you are including eukaryotes, you should take care of possible introns within the eukaryotic sequences.
Second, what gene your sequences encode? is it a protein-coding gene or not? well, depending on this you might probably want to cluster your sequences at an appropriate sequence similarity (or identity) value, and then select only a representative of each resulting cluster. However, it is not clear how to define an identity threshold to do this for any gene sequence and even more problematic can be when you are mixing prokaryotic and eukaryotic sequences. For clustering tools you might want to take a look at this question here in RG:
https://www.researchgate.net/post/Clustering_BLAST_search_results_by_species
That is all I can recommend with the information that you have provided.
Best regards.
Select them on the basis of their informativeness for the hypothesis you wish to test:
Article Profiling Phylogenetic Informativeness
Article Optimal Selection of Gene and Ingroup Taxon Sampling for Res...
Article Phylogenetic informativeness profiling of 12 genes for 28 ve...
Article PhyDesign: An online application for profiling phylogenetic ...
Article Experimental Design in Phylogenetics: Testing Predictions fr...
Article The Probability of Correctly Resolving a Split as an Experim...
Article Phylogenetic Signal and Noise: Predicting the Power of a Dat...
Conference Paper Phylogenetic experimental design
Article PhyInformR: phylogenetic experimental design and phylogenomi...
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