# Relax Nuclear metabolism genes
###### tags: `sloth`

- Table of Content
[ToC]

I ran an orthofinder before with whole-genome-predicted proteins for:

| ID | Column 2 |
| -------- | -------- |
| mOrnAna1 | platypus |
| bostaurus | cattle |
| cfam_lcl | dog |
| Dasnov3 | dasypus novemcinctus |
| GRCh38 | Homo sapiens |
| GRCm39 | Mus musculus |
| koala | koala |
| Loxafr3 | elephant |
| mChoDid1 | Choloepus didactylus |
| Mhudiblu | Bonobo |
| Mmur_lcl | grey mouse lemur |
| MonDom5 | gray short-tailed opossum |

# 1- Testing relax on glucose-6-phosphate_isomerase

Hyphotesis is that this is not relax on the sloth

So I fond the orthogroup, got the protein sequences, then the nucleotide sequences. Then I needed to generate the codon aligment

## 1.1 Using codon-msa for codon aligment

https://github.com/veg/hyphy-analyses/blob/master/codon-msa/README.md

With codon msa one (i) takes the nucleotide sequences and run through pre-msa to correct frame-shift mutations and translate the resulting sequences to proteins. Then (ii) Take the output of step 2 and run in through the general MSA program to generate a protein MSA. Finally (iii) Run the protein MSA and the frameshift corrected nucleotide sequences from step 2 through post-msa.bf to obtain a nucleotide msa.

*** Attention

This is different than what Jacky has ran. Jacky, can you confirm with your colaborators that this is an ok aligment for hyphy? ****

### 1.2 Input it to Hyphy

I ran it on the browser first just for a test. This was the tree. Any way I can rot but the platypus???


### 1.2.2 Test branch

Jac, was I correct in choosing the sloth in the branch selection?

### 1.2.3 Results

You say (k<1 indicates relaxation, k>1 indicates intensification). I'll look into the method, but do these results seem sane to you?






# 2. Oxidative_phosporilation

Longest Choloepus didactylus isoforms through kEGG


## 2.1. K00234
succinate dehydrogenase (ubiquinone) flavoprotein subunit


## Test for relaxation (or intensification) of selection [RELAX]
Likelihood ratio test **p =   0.1491**.
>No significant evidence for relaxation (or intensification) of selection among **test** branches _relative_ to the **reference** branches at P<=0.05

### 2.1.1 OG0004707

>No significant evidence for relaxation (or intensification) of selection among **test** branches _relative_ to the **reference** branches at P<=0.05

Ideas, lots of these metabolism genes seem to be single copy. So why not run the selection analysis for all the single copy at once?!