ND2 tree

Procedure

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

In this case the marker ND2 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; ND2 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

The code was produced and adjusted using the following codes

Code	Species
KP777815.1	Eunicea mammosa
AY126379.1	Eunicea fusca
KP777810.1	Eunicea laciniata
AY684593.1	Eunicea clavigera
KP777816.1	Eunicea calyculata
KP777813.1	Eunicea tayrona
AY684592.1	Eunicea asperula
AY126378.1	Eunicea tourneforti
AY126376.1	Eunicea knighti
AY684587.1	Eunicea laxispica
AY684588.1	Eunicea succinea
KP777812.1	Eunicea pallida
AY126382.1	Plexaura homomalla
AY126385.1	Plexaurella grisea
AY126384.1	Plexaura kuna
AY684590.1	Plexaura flexuosa

(Plexaura kuna,(((Eunicea succinea,Eunicea laxispica),(Eunicea calyculata,Eunicea mammosa)),((((Eunicea knighti,(Eunicea fusca,Plexaura flexuosa)),(Eunicea tayrona,Eunicea pallida)),(((Eunicea clavigera,Eunicea laciniata),Eunicea asperula),Eunicea tourneforti)),Plexaura homomalla)),Plexaurella grisea):0.0;

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 ND2 marker Since this tree was made with only one marker and one sequence from each species the results are not conclusive.

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