Ben HallerSLiM Workshop at Harvard, August 28th to September 1st, 2023. Applications are open now. Biology peeps, please share! https://groups.google.com/g/slim-discuss/c/UDtAsNFlkiE
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| github | https://github.com/gwct |
Gregg Thomas
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Bioinformatics Scientist at Harvard FAS Informatics. Recent postdoc at UMontana (http://thegoodlab.org). Evolution, Genomics, Phylogenetics. Dog walker. He/him.
@photocyte @timsackton
Specifically:
python degenotate.py -a [annotation file] -g [genome fasta file] -la [output file for amino acid sequences] -o [output directory]
would do exactly what you described!
@photocyte Our tool (w/ @timsackton), degenotate, may do what you need. It can extract sequences and limit output to longest isoform. If you have other criteria you’d like to output by, let us know with an issue on the repo!
Daren Card, Ph.D.I'm at #PAG30 in San Diego! Speaking about limb reduction in #reptiles in #Genomics of Non-Classical Model Animals. 10:55am Sun. Jan. 15 in Pacific E. Thanks to Marc Tollis 4 organizing & invitation! Looking forward to seeing friends and meeting new people! DM if you would like to meet up! #MuseumGenomics
@KatieEmelianova @timsackton Thanks! We haven't implemented a coding model yet, but it could still be used on coding sequences. But it might be a good idea to limit to coding sites that we assume evolve similarly (e.g. 4-fold degenerate sites).
Holiday #preprint from us!
https://www.biorxiv.org/content/10.1101/2022.12.23.521765v1
Have you ever wanted to test for accelerated substitution rates while accounting for #phylogenetic discordance? #PhyloAcc-GT can do that! Great to work with Han Yan, Zhirui Hu, Scott Edwards, @timsackton, and Jun Liu!
More about the software can be found here: https://phyloacc.github.io
Jeremy B. Yoder 🖖🏻🌿🏳️🌈📈In the Molecular Ecologist: Four science books for 2022 https://www.molecularecologist.com/2022/11/28/four-science-books-2022-tree-thieves-geology-haldane-animal-senses/
#books #evolution #genetics #conservation #forest #geology #MolecularEcologist
Ben FultonOur new software is out!
"Here, we present a new software package (CAGEE) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. In contrast to previous methods that treat each gene independently, CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene."
@benfulton I ran into the same thing recently and found that if I use --packages <package name of the recipe I just added> instead of --git-range it will work with my fork.