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Description:
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Utilizing the large amount of biological sequences data from the databases is a powerful tool for molecular phylogenetics . But dealing with the storage and analysis of the sequence data is tedious with manual methods , especially when tens of thousands sequences need to be analyzed . To address this problem , I developed the automatic framework for general molecular phylogenetics analysis (AGMPA ) system . The system automates the process of the routine work in molecular phylogenetics . Perl scripts were used to glue together the programs used and to parse analysis outputs . This system also implements databases for information storage , retrieval and presentation . The databases integrate different types of data in molecular phylogenetics and supports database query from different ways . The system provides a graphical user interface (GUI ) for all the functions and for calling bioinformatics programs of BLAST , FASTA , CLUSTAL , Phylp and TREE -PUZZLE . The system is implemented with perl /TK to ensure its cross -platform compatibility . The system was tested with 52 ,499 nucleotide sequences and 1165 protein sequences from Gossypium genus and with 36 ,495 protein sequences from Poaceae family . Phylogenetic analysis results from these two test datasets are presented . |