How to make a robust amino acid phylogeny with adequate robustness support This is the second part of this thread:  Duplicated genes and genome fragmentation

As @Michael G. suggested, I did a pseudo-annotation of sequences 5-2 and 5-3 (i.e., I joined both sequences into one) and I did the phylogenetic analysis again. Here is the tree that I obtained: 



Both of my sequences are shown in a red rectangle. The length of the branch seems to have decreased a bit. Also, I looked at the branches near sequence 5-1. One of them is the original query sequence from species A and the other one is a hypothetical protein from the same species (probably related to the query sequence, but I couldn't find any domains because it is only a few amino acids long). I still need to find the root of the phylogeny but I am not sure how to do this...
To finish you need bootstrap support using a model-based tree building algorhithm, I use RAxML, specifically raxmlHPC (easily downloadable and compiles on Linux and OSX). The codes are quite complicated and I've given them below. 

A robust maximum likelihood tree is,

raxmlHPC -m PROTGAMMAILG -n output.tre -o outgroup-p 10000 -s alignment_file.phy


To make a bootstrap tree,

raxmlHPC -b 459 -m PROTGAMMAILG -n output.tre -o outgroup -p 10000 -s /path_to_alignment.phy -N 500


Make a consensus tree of the bootstraps,

raxmlHPC -f b -m PROTGAMMAILG -n output.tre -o outgroup -p 10000 -t /path_to_master_tree(best_tree) -z path_to_bootfile


You require bootstrap support >80% and please repeat this with and without 5-2/5-3 (it still looks long)

You need a fairly robust desktop, dedicated for around 24 hours to complete one calculation. You have enough results to draw a conclusion.

Viewing the tree, FigTree is easy.

Root

Check the work of Cavalier-Smith, he heavily focused on basal protists to find a species which evolved, using external evidence, before any other member of your group. One of the ingroups may have sufficient evidence to say it evolved before the rest and that is your root, which you select as an outgroup.