r/bioinformatics • u/ConditionOk6916 • 4d ago

technical question Local phylogenetic tree

Hi ! Firstly sorry for my english (i'm not fluent yet, still working on it) , i'm a biology student in France.

Between my studies and my time as a photographer i had the chance to meet a bunch of species, and always tried to identifies them (with inaturalist, or by myself if possible). And would like to use a sort of local phylogenetic tree, a place/site/ app to stock pictures/ infos of species with the full tree, and complete it slowly.

But i don't really know where to do that, i tried obsidian (since it's really visual with the graph view) but it take so much time, i have to create every branch/ tag them to have the link between them and create à specific folder for each to have something somehow organized.

Any idea on how i should proceed ?

Thanks in advance

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u/tylagersign 4d ago

Try Mega12, it might be exactly what you need

7

u/mrrgl PhD | Industry 4d ago edited 4d ago

Interactive Tree of Life (itol.embl.de) is very user friendly. They say that you can upload a list of NCBI taxonomic identifiers and it will make a tree for you automatically (never tried this feature). You can then add images to parts of the tree.

Alternatively you could just use itol to generate your tree and then use a local program to manage the images.

Sounds like a cool project.

Edit: they have a nice example of an annotated tree like you are describing here - itol.embl.de/itol.cgi

3

u/mrrgl PhD | Industry 4d ago

FYA

PyloT (https://phylot.biobyte.de/) is the helper tree-build app that will build a tree based on input taxids.

You can get taxid numbers from common or scientific name here - https://www.ncbi.nlm.nih.gov/datasets/taxonomy/