fredericlemoine

Hello, That is something I wanted to work on for a long time. The commits solve part of the drawing issues (especially with "normal" layout), but there are still work...

Sure, I will do it soon. In the mean time, you can also open your svg files with inkscape, and modify the dimension of the image.

I see. First of all, `gotree collapse length` removes _internal branches_ that are shorter than a given threshold. For example: ``` $ echo "((A:0.2,B:0.2):0.1,C:0.2,D:0.2);" | gotree collapse length -l 0.2...

I added options `--root`and `-tips` to `collapse brlength`, you can have a look at the [command documentation](https://github.com/evolbioinfo/gotree/blob/master/docs/commands/collapse.md). This [pre-release](https://github.com/evolbioinfo/gotree/releases/tag/v0.4.1c) implements it. Let me know if it solves your issue.

Thanks for the suggestion, You can test `gotree rename` `--rm-quotes` and `--add-quotes` options in the latest [v0.4.1a](https://github.com/evolbioinfo/gotree/releases/tag/v0.4.1a) pre-release . Moreover, for the spaces in node/tip names, would the following command...

Hi @tseemann , Can I close this issue? Could you test it? Thanks

I am in the same situation for running a workflow with thousands of samples, and would need dozens of TB. Lots of bam files are needed only by 2 steps...

Hi Romain, Thanks for using goalign and for your suggestion. How would you compute this conservation score? Would it be, for a given column, the number of sequences that are...

Hi Romain, I think I understand, thanks for the suggestion. I tried with the option `--char` to `goalign clean sites`. * WIth `--char MAJ --cutoff 1`, it will remove sites...

Thanks @jean-baka and @tseemann for your interesting comments. I indeed thought about alignment trimmers, I should have mentioned them in my first comment. And maybe even just for removing sites...