[ Python ] I need help building 6 gene trees -- 6
Budget: ₹600 – ₹1,500 INR
I need help building 6 gene trees.
I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees should be clear and make sense. For each tree, I need notes about the tree production like removal of specific sequences, branches, alignments, trimming etc. so the data is reproducible.
- here is a zip of sequences for the genes (.pep for peptide and .cds for coding file)
some sequences are longer than others
I aligned the files with MAFT.
If you need to realign or trim files, that's alright.
They just need to have the stop codons (aka. the full protein)
- RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores.
https://github.com/amkozlov/raxml-ng
- I use Linux and biopython interchangeably
Thank you.
I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees should be clear and make sense. For each tree, I need notes about the tree production like removal of specific sequences, branches, alignments, trimming etc. so the data is reproducible.
- here is a zip of sequences for the genes (.pep for peptide and .cds for coding file)
some sequences are longer than others
I aligned the files with MAFT.
If you need to realign or trim files, that's alright.
They just need to have the stop codons (aka. the full protein)
- RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores.
https://github.com/amkozlov/raxml-ng
- I use Linux and biopython interchangeably
Thank you.