COI tree

Procedure

First a document was made with all the sequences for the Gene I was looking at

In this case the marker COI was used for all of the species of coral that I have been using in the PCRs

here are a list of all the codes used; COI sequences

These were then shortened to be the samelength and aligned using the program AliView https://ormbunkar.se/aliview/

Then using the website Cipres https://www.phylo.org the aligned sequences were analysed using the RAxML-HPC2 on XSEDE tool to create a Phylogenetic tree using maximum likelihood

This produced the following code

(Eunicea tourneforti(Eunicea tourneforti(((Eunicea succinea,Eunicea clavigera),Eunicea calyculata),(((((Eunicea fusca,Eunicea calyculata),Eunicea fusca),Eunicea fusca),(((Eunicea flexuosa,(Eunicea flexuosa,Eunicea flexuosa)),(Eunicea flexuosa,(Eunicea laxispica,Eunicea flexuosa))),Eunicea tourneforti)),Eunicea tourneforti))),Eunicea calyculata);

the names were then adjusted using the following codes

Code	Species
MK153456.1	Eunicea succinea
MK153476.1	Eunicea flexuosa
MK153442.1	Eunicea flexuosa
MK153329.1	Eunicea flexuosa
MK153303.1	Eunicea flexuosa
MK153374.1	Eunicea flexuosa
MK153441.1	Eunicea laxispica
MK153417.1	Eunicea tourneforti
MK153414.1	Eunicea tourneforti
MK153408.1	Eunicea tourneforti
MK153376.1	Eunicea tourneforti
MK153406.1	Eunicea fusca
MK153362.1	Eunicea fusca
MK153308.1	Eunicea fusca
MK153384.1	Eunicea clavigera
MK153378.1	Eunicea calyculata
MK153334.1	Eunicea calyculata
MK153432.1	Eunicea calyculata

finally using the site ITOL https://itol.embl.de a tree was made:

This tree can be shown in other ways as well

ignoring branch length:

Circular:

Uprooted:

Analysis

This tree shows the maximum liklihood tree for the COI marker This tree has multiples of the same species to see how that effects the tree it is still only done with one marker

That is why in the study I am conducting many markers will be used and multiples of each species as well