Doubts regarding phylogeny analysis with protein sequence
1. While making a phylogenetic tree with a protein sequence is it ok if I include sequences inferred from homology?
In the uniport, there are protein sequences of 4 categories: those that have evidence at protein level, transcript level, derived from homology and just predicted sequences. My question is if I include the sequences inferred from homology to the analysis, will it affect the reliability of the tree and ancestor sequence?
2. After Clustal analysis and MEGA analysis how can I obtain the probable ancestor protein sequence?
3. While going for the determination of ancestor sequence and/or consensus sequence can we include the outgroup too?
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lia.elias •
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