# mafft does not work inside my Qiime2 environment

**URL:** https://forum.qiime2.org/t/mafft-does-not-work-inside-my-qiime2-environment/19267
**Category:** Technical Support
**Tags:** conda, mafft
**Created:** [April 18, 2021, 5:07am UTC](https://forum.qiime2.org/t/mafft-does-not-work-inside-my-qiime2-environment/19267 "2021-04-18T05:07:22Z")
**Posts on this page:** 1
**Showing post:** 4

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### Author: ![andrewsanchez](https://forum.qiime2.org/user_avatar/forum.qiime2.org/andrewsanchez/32/20160_2.png) [@andrewsanchez](https://forum.qiime2.org/u/andrewsanchez)
#### Post date: [April 20, 2021, 4:50pm UTC](https://forum.qiime2.org/t/mafft-does-not-work-inside-my-qiime2-environment/19267/4 "2021-04-20T16:50:13Z")

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When it comes to the `PATH` variable, the order of items matters. You can see below that the `mafft` installation external to your qiime 2 conda environment appears before the qiime 2 environment. It's important that the qiime 2 environment comes first. Otherwise, your computer will favor programs that appear earlier in the list.

`PATH=/opt/local/bin/mafft:/Users/m213406/Filtlong/bin:/Users/m213406/nanotimeparse:/Users/m213406/NanoOK/bin:/opt/local/share/arb/bin:/opt/local/bin:/opt/local/sbin:/Users/m213406/opt/anaconda3/envs/qiime2-2021.2/bin:/Users/m213406/opt/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/m213406/centrifuge/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin:/opt/X11/bin`

Usually, the `PATH` variable is configured in the `~/.bash_profile` on mac os, but it could be conifigured elsewhere like in `~/.zshrc`. The way to fix this is figure out where `PATH` is being set, and to remove the line that is prepending `mafft` to the variable. For example, if you find the following line in your `~/.bash_profile`:

```bash
export PATH=/opt/local/bin/mafft:$PATH

```

This would prepend that specific `mafft` installation. In this case, you could just remove that line entirely.

Note that there are also several other items which appear at the beginning of the list, prior to the `qiime2` bit. This may or may not cause problems, but is often a sign of a less than ideal approach to configuring `PATH`.

I hope that helps! Good luck, and let me know how you get along.

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