---
title: Comparing reference genomes with Mauve

tags: OMM
description: Personal hackmd notes
image: https://partechshaker.com/wp-content/uploads/2018/10/logo_square.png
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GA: UA-165598729-1
---

---

[TOC]

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Comparing reference genomes with _Mauve_
===

[Mauve](http://darlinglab.org/mauve/mauve.html) is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

**Howto read these plots**:
> The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line. Colored block outlines appear above and possibly below the center line. Each of these block outlines surrounds a region of the genome sequence that aligned to part of another genome, and is presumably homologous and internally free from genomic rearrangement. When a block lies above the center line the aligned region is in the forward orientation relative to the first genome sequence. Blocks below the center line indicate regions that align in the reverse complement (inverse) orientation. Regions outside blocks lack detectable homology among the input genomes. Inside each block Mauve draws a similarity profile of the genome sequence. The height of the similarity profile corresponds to the average level of conservation in that region of the genome sequence. Areas that are completely white were not aligned and probably contain sequence elements specific to a particular genome. The height of the similarity profile is calculated to be inversely proportional to the average alignment column entropy over a region of the alignment.

more details on [their website](http://darlinglab.org/mauve/user-guide/viewer.html)

Installation
---

wget http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64/mauve_linux_snapshot_2015-02-13.tar.gz
cd ~/Download/
tar xvzf mauve_linux_snapshot_2015-02-13.tar.gz
cd mauve_snapshot_2015-02-13
./Mauve

On Mac just open `Mauve.ap`

**I46** *C. innocuum* (Firmicutes)
---

cd /home/aime/projects/oligomm-claudia/reference_comparison
/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=i46.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/C_innocuum_I46.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/i46.fasta


**YL44** *A muciniphila* (Verrucomicrobia)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl44.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/A_muciniphila_YL44.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl44.fasta


**KB18** *A muris* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=kb18.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/A_muris_KB18.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/kb18.fasta


**YL2** *B animalis* (Actinobacteria)
---

==should this not *B. longum*?==

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl2.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/B_animalis_YL2.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl2.fasta


**I48** *B caecimuris* (Bacteroidetes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=i48.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/B_caecimuris.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/i48.fasta


**YL58** *B coccoiedes* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl58.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/B_coccoiedes_YL58.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl58.fasta


**YL32** *C. Clostridioforme* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl32.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/Clostridioforme.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl32.fasta


**KB1** *E faecalis* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=kb1.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/E_faecalis_KB1.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/kb1.fasta


**YL31** *F plautii* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl31.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/F_plautii.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl31.fasta


**I49** *L reuteri_I49* (Firmicutes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=i49.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/L_reuteri_I49.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/i49.fasta


**YL27** *M intestinale* (Bacteroidetes)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl27.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/M_intestinale_YL27.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl27.fasta


**YL45** *T muris.fasta* (Proteobacteria)
---

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=yl45.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/T_muris.fasta /home/aime/projects/oligomm-claudia/data/annotation/fasta/yl45.fasta


New reference genomes
---

Not sure if we need the ` --collinear` parameter?

/home/aime/Downloads/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=all_new.xmfa /home/aime/projects/oligomm-claudia/databases/omm_new/joined_reference_curated.fasta --collinear