Why does iqtree not like / in sequence names?

[James]

Hi,

I'm wondering why iqtree doesn't like / in sequence names and if this can be changed in a future release?

Influenza uses / to separate information in the sequence title like A/chicken/Spain/1234/2018 but they all get replaced by underscores by iqtree.

I can open the *.treefile with a text editor and replace all _ with / to put it back but it would be nice not to have to.

Thanks

James

[James]

I just saw the release notes for 1.6.6
I haven't tried it yet but sounds like you've already fixed this.

Thanks
James

[Minh Bui]

Hi James,

The character replacement will still occur with v1.6.6. The deep reason is because internally IQ-TREE uses BIONJ code to infer a neighbor-joining tree, and this code does not like such characters… since several users asked about this, we look at it in a future release (but not with high priority as this is not a bug).

Under Linux or Mac OS, you can use a command line to replace _ by / using, for example, sed command:

sed ’s/_/\//g’ TREEFILE

Thanks for your understanding,

Minh

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