Phylogenetic tree rebuilding method for building sub trees on basis of big trees

A large tree and sub-tree technology, applied in the field of phylogenetic tree reconstruction, can solve the problems of inconvenient retrieval and utilization

Active Publication Date: 2015-04-29
COMP NETWORK INFORMATION CENT CHINESE ACADEMY OF SCI
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Problems solved by technology

The characteristics of its text files, in practical applications, especially in big data such as the tree of the evolutionary basis of terrestrial plant systems in China, its retrieval and

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  • Phylogenetic tree rebuilding method for building sub trees on basis of big trees
  • Phylogenetic tree rebuilding method for building sub trees on basis of big trees
  • Phylogenetic tree rebuilding method for building sub trees on basis of big trees

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Embodiment Construction

[0037] The present invention will be further described below through specific embodiments and accompanying drawings.

[0038] The basic evolutionary tree in this embodiment is the basic tree data Setbig of Chinese terrestrial plant phylogeny, and the source of its standardized basic species list is "Flora of China" (Wu ZY, Reven P, and Hong DY (eds.).1994 -2013.Flora of China.Beijing:Science Press and St.Louis:Missouri Botanical Garden Press.). Its format is newick format, as shown in Table 2.

[0039] See attached figure 1 , 2 The specific process of the reconstruction method of the phylogenetic tree described in this embodiment is:

[0040] Step A: Analysis and segmentation of the large tree of the evolutionary basis of terrestrial plants in China: In this embodiment, the file of the large tree of the evolutionary basis of terrestrial plants in China is selected for segmentation and reconstruction, and the number of divisions and division weights are recorded, converted i...

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Abstract

The invention discloses a phylogenetic tree rebuilding method for building sub trees on the basis of big trees. The method comprises the following steps that (1) a phylogenetic basic big tree is divided, and the division times, the division weight values and the relationship chain of each leaf node are recorded and are then stored into a database; (2) a species sub directory list is determined according to the species name in a species sub directory, and a matched node element list is found in the database, and a mapping relationship between the sub directory list and the node element list is built; (3) the relationship chain and the node weight value of each node element in the node element list are retrieved in the database; (4) the relationship chains are compared in pairs for forming node element grouping relationship; (5) according to the node weight values and the grouping relationships of the node elements, the corresponding weight value of each node element in a phylogenetic sub tree is calculated, and the phylogenetic sub tree corresponding to the species sub directory is generated and outputted. The phylogenetic tree rebuilding method has the advantage that the requirement of fast building organism evolutionary relationships in the biological samples according to the directory and the like can be met.

Description

technical field [0001] The invention belongs to the technical field of applied bioinformatics, and in particular relates to a phylogenetic tree reconstruction method based on a large tree to construct a subtree, which is mainly used in related fields such as biological phylogeny, biological barcode, biological species identification, ecological quadrat evolutionary tree reconstruction, etc. A method of reconstructing and visualizing the phylogenetic subtree based on the phylogenetic base tree of big data. Background technique [0002] The phylogenetic tree is also called the phylogenetic tree (phylogenetic tree), which uses a tree-like branch graph to represent the relationship between various (class) organisms, and speculates on the evolutionary history of species through the study of biological sequences. The phylogenetic tree is mainly constructed through DNA sequence, protein sequence, protein structure, etc., or the structural evolution tree is established through prote...

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Application Information

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IPC IPC(8): G06F19/14G16B10/00
Inventor 孟珍黎建辉周园春王学志
Owner COMP NETWORK INFORMATION CENT CHINESE ACADEMY OF SCI
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