Concatenation_approach.Rmd

---
title: "Concatenation Approach"
output: github_document
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
                      eval = FALSE,
                      fig.path  = "figures/",
                      out.width = "50%")
```

**Author**: [Léo-Paul Dagallier](https://github.com/LPDagallier)    
**Last update**: `r format(Sys.Date())`

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In the concatenation approach we will first concatenate the MSAs of all the loci into a single MSA (or 'supermatrix'), and then infer the species tree from the supermatrix.

Here we'll present species tree inference with [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) and [IQ-TREE](http://www.iqtree.org/). With RAxML, the MSAs for all the loci need to be concatenated into a single supermatrix prior to RAxML inference. With IQ-TREE, we can directly input all the MSAs files that will be concatenated internally by IQ-TREE.

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## Infer tree with IQ-TREE


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Under construction, more coming soon. (feel free to send me an email or open an issue to pressure me)


Draft:

To concatenate matrices: https://github.com/marekborowiec/AMAS/