Phylogenetic trees using neighbor-joining analysis with maximum composite likelihood method and bootstrap values were constructed by using MEGA5.2 software (http://www.megasoftware.net/).net/
The amino acid sequences of invertebrates and vertebrates were aligned using ClustalW v2 software [ 49] and neighbor-joining trees with bootstrap values were constructed for phylogenetic analyses using the MEGA v6 software [ 50].
Strict consensus trees were constructed, and bootstrap values were calculated as measures of branch support [ 79] using the following bootstrap parameters: 100 bootstrap replicates, 5000 MAXTREES per replicate, random addition sequence, TBR, STEEPEST DESCENT, and MULTREES.
The genealogical tree was constructed and its bootstrap values were computed using the program FreeTree.
Six members, namely PaAse1, PaMnt2, PaCrp2, PaClk2, PaE spl 2 and PaE spl 3, were identified with sufficient confidence for all the bootstrap values were over 50 in all the constructed trees.
Maximum-likelihood trees were constructed with PhyML 2.4.5 software and bootstrap values were obtained for 1,000 replicates [ 74].
Although phylogenetic trees can be constructed, subsequent confidence metrics such as bootstrap values are low, suggesting that these trees may be unreliable predictions of gene relationships [ 37, 38].
Maximum-likelihood phylogenetic trees were constructed by using PhyML version 3.0 (8 ), and bootstrap values were calculated from 1,000 trees.
The constructed tree was tested by the bootstrap method and bootstrap values are depicted adjacent to each node.
A maximum parsimony tree with branch confidence values based on 1000 bootstrap replicates was constructed.
