Issue using IQ-Tree for branch length estimation

Akshay Ravoor

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Apr 17, 2024, 8:07:27 PM4/17/24

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Hello All,

I am an undergrad trying to use IQ-Tree to re-estimate branch lengths for a tree with a known topology and known sequences for all nodes (root, internal nodes, and leafs). The tree is relatively small with just 32 leafs. I am not sure where the original branch lengths in the file came from so I would like to re-estimate them with IQ-Tree under the WAG model for a downstream task.

Below is the command I am using (file paths omitted), and attached are the relevant files (FASTA + newick). IQ-Tree tells me that none of my internal node alignment sequences ('I1', 'I2',...,'I31') are present in the tree even though I have confirmed through various methods that my newick is properly formatted to label the internal nodes as such (like printing out all the node names with biopython ingesting the newick).

bin/iqtree2 -s all_nodes_aligned.FASTA -te gt.newick -m WAG+G -nt AUTO --keep-ident

> ERROR: Alignment sequence I1 does not appear in the tree

> ...

> ERROR: Alignment sequence I31 does not appear in the tree

When I delete the internal node sequences from the FASTA the run finishes without issue, but I want IQ-tree to estimate branch lengths based on the ancestral sequences as well (not just the leafs).

Does anyone have any idea what is going wrong? I am a novice in this area, so please let me know if I am doing anything incorrectly.

Thank you!

--

Sincerely,

Akshay

all_nodes_aligned.FASTA

gt.newick

Bui Quang Minh

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Apr 18, 2024, 3:09:35 AM4/18/24

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Hi Akshay, Yes I know why ;-) All phylogenetic reconstructions only
take sequences at the tip of the tree. You don't need to provide any
ancestral sequences.

There is an option -asr in IQ-TREE
(http://www.iqtree.org/doc/Command-Reference#ancestral-sequence-reconstruction)
that allows you to infer ancestral sequences, though that's not what
you are after.

Cheers
Minh

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Akshay Ravoor

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Apr 18, 2024, 6:23:09 PM4/18/24

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Hi Minh,

Understood, thank you very much!

--

Sincerely,

Akshay

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