CBCAnalyzer Inferring phylogenies based on compensatory base changes (CBCs)
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CBCAnalyzer Tags

simulate phylogenies phylogenies simulation estimate large phylogenies large phylogenies estimation large phylogenies analysis compensatory base change CT Transform CBC Detect CTTransform CBCDetect CBCTree

CBCAnalyzer Description

The CBCAnalyzer (CBC = compensatory base change) was developed to be a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats (ct, RNAviz ct or Mac ct), and generates a so called ``bracket-dot-bracket'' format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. Herewith we count for CBCs in all against all of the aligned sequences, which is important in detecting species, discriminated on their sexual incompatibility. The count (distance) matrix obtained by CBCDetect is used as input for CBCTree that reconstructs a phylogram by using the algorithm of BIONJ.NOTE:CBCAnalyzer is freely available for non-commercial use

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