PTPRJ+Phylogenetic+Trees

Phylogenetic Trees & Bootstrap Analysis

A genomic tool, **MEGA 5 Beta 4﻿ **is designed for conducting automatic and manual sequence alignments, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. In this case, MEGA 5 was used to determine phylogeny, evolutionary relationships, and maximum parsimony analyses of the homologous proteins produced by several species.

**Figure 1.** Molecular Phylogenetic anaylsis by Maximum Likelihood method The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model. The tree with the highest log likelihood (-6117.1763) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites is < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 7 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.

**Figure 2.** Evolutionary relationships of taxa The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 1.29747661 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The analysis involved 7 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.

**Figure 3**. Maximum Parsimony analysis of taxa The evolutionary history was inferred using the Maximum Parsimony method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The MP tree was obtained using the Close-Neighbor-Interchange algorithm (pg. 128 in ref.) with search level 2 in which the initial trees were obtained with the random addition of sequences (10 replicates). The analysis involved 7 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.

**Figure 4.** Evolutionary relationships of taxa The evolutionary history was inferred using the Minimum Evolution method. The optimal tree with the sum of branch length = 1.29747661 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm at a search level of 0. The Neighbor-joining algorithm was used to generate the initial tree. The analysis involved 7 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.

**Figure 5.** Evolutionary relationships of taxa The evolutionary history was inferred using the UPGMA method. The optimal tree with the sum of branch length = 1.29313370 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The analysis involved 7 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 723 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.

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