Prevent truncation of taxa names

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Brittany Rife Magalis

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Jul 9, 2019, 8:43:48 PM7/9/19
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Thanks in advance for dealing with this, but I was wondering if there was an argument for preventing iqtree from truncating lengthy taxa names or at least specifying the length they can be? Attached is an example where, rather than the accession numbers alone, I am needing to keep the clone, isolate IDs, and country of origin information following. I know this is something I can easily do using a scripted find and replace, but I was just curious as to whether there was a solution that could simply be used during iqtree execution alone. Thanks again!
final_HIVenv_calign.fasta

Minh Bui

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Jul 10, 2019, 11:57:07 PM7/10/19
to IQ-TREE, Brittany Rife Magalis
Hi,

There is no way to do that. When reading a FASTA file, IQ-TREE will discard parts of the sequence name after the first empty space or tab character. Because this is typically extra description. You can, as you said, replace empty spaces with underscore to keep the rest part of the names.

Cheers
Minh

On 10 Jul 2019, at 10:43 am, Brittany Rife Magalis <brma...@gmail.com> wrote:

Thanks in advance for dealing with this, but I was wondering if there was an argument for preventing iqtree from truncating lengthy taxa names or at least specifying the length they can be? Attached is an example where, rather than the accession numbers alone, I am needing to keep the clone, isolate IDs, and country of origin information following. I know this is something I can easily do using a scripted find and replace, but I was just curious as to whether there was a solution that could simply be used during iqtree execution alone. Thanks again!

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