User: tim_mci

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Posts by tim_mci

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Answer: A: Visualise node-defining SNPs on a phylogeny
... Thank you heaps for that, it should help with my human mtDNA data! ...
written 3.4 years ago by tim_mci0
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Visualise node-defining SNPs on a phylogeny
... Hi all, I have an alignment in fasta format and a phylogenetic tree in Newick format. I am looking for a way to visualise/map the character state changes or SNPs to the node/branches they define. Any suggestions on available software that does this? Thanks in advance, Tim. ...
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Annotation of position in an Open Reading Frame from a list of sites
... Hi all, I am working human mitochondrial sequence data (predominantly using R). I am looking for a tool to quickly annotate if any given site falls in the 1st, 2nd, or 3rd position in a codon (if they fall in an Open Reading Frame at all). I have full mitochondrial sequences in fasta format, as wel ...
open reading frame annotation reading frame written 3.7 years ago by tim_mci0
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Export inferred ancestral sequence using MEGA
... Hi all, I've used MEGA6 to infer the ancestral states of a given site. The MEGA5 citation (Tamura et al., 2011) states that ancestral sequences can be reconstructed. However, I am unable to find how to view the inferred ancestral sequence, let alone export it. Any tips? Thank you in advance, Tim ...
phylogenetics mega written 3.9 years ago by tim_mci0
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Comment: C: Pruning phylogenetics trees to reduce complexity
... Hi Brice, I checked it out, not exactly what we're looking for in this instance, but thanks for the suggestion, looks like it will come in handy in the future! Thank you! ...
written 3.9 years ago by tim_mci0
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Pruning phylogenetics trees to reduce complexity
... Hi all, I've been searching with no luck for a tool to reduce the complexity of a phylogenetic tree I've produced, that has 128 taxa. I need a tool to prune the number of taxa down, preferably by branch length or distance matrix. I have tried using Network by Fluxus, however this was only able to ...
phylogenetics written 3.9 years ago by tim_mci0 • updated 3.9 years ago by Brice Sarver3.0k

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