# Tools for concatenating individually aligned loci into a supermatrix for downstream analysis

**URL:** <https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489>\
**Category:** usegalaxy.eu support\
**Tags:** maf-manipulations\
**Created:** [November 13, 2025, 4:31am UTC](https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489 "2025-11-13T04:31:58Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![ground\_pearl\_girl](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ground_pearl_girl/32/7440_2.png) [@ground\_pearl\_girl](https://help.galaxyproject.org/u/ground_pearl_girl)\
**Post date:** [November 13, 2025, 4:31am UTC](https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489/1 "2025-11-13T04:31:58Z")

</div>

I am attempting to create a concatenation-based phylogeny - which requires each of the individually aligned loci to be concatenated into a supermatrix - but I am struggling to find tools available in Galaxy to do this.

Could you please provide some guidance of which tools are available and compaible with IQ-Tree? Alternatively, could tools (e.g., SCaFoS, PHYLUCE, AMAS, SPLACE) be installed so I can complete this step?

Thank you!

---

<div class="post-metadata">

**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [November 13, 2025, 7:26am UTC](https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489/2 "2025-11-13T07:26:24Z")

</div>

Hi @ground_pearl_girl

I probably misunderstood the topic, but do you mean something similar to [MAF](https://genome.ucsc.edu/FAQ/FAQformat.html#format5) blocks? If yes, try Join MAF blocks by Species.

Kind regards,

Igor

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [November 13, 2025, 6:03pm UTC](https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489/3 "2025-11-13T18:03:17Z")

</div>

I agree with @igor

An example is in the 2012 publication linked in this topic.

The topic also includes a recent example history for a few of the tools, but the full protocol in the publication is still possible (including the multi-species filtering and merging). The only difference is that you will need to supply the _reference_ multi-way conservation data yourself from the history. UCSC is one source.

Any questions, please ask! 🧑‍🔬

> [@MAF tools in Galaxy: step by step publication with an example shared history](https://help.galaxyproject.org/t/attempting-to-use-stitch-maf-blocks-tool-but-lack-of-documentation/10091):
>
> Hello, I am trying to provide a list of input coordinates so that I can use this tool to stitch together existing MAF blocks, but it is surprisingly complicated. I don’t understand why galaxy is insisting that the “choosing intervals” input is a file (shouldn’t it just be intervals, such as (1,6)? I’m also not sure what to put for MAF type. Any help would be immensely appreciated, thank you!

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [April 18, 2026, 12:32am UTC](https://help.galaxyproject.org/t/tools-for-concatenating-individually-aligned-loci-into-a-supermatrix-for-downstream-analysis/16489/4 "2026-04-18T00:32:41Z")

</div>