zxjsdp / bioinfo-scripts

Scripts used for bioinformatics and phylogenetics.

bioinfo-scripts

Scripts used for bioinformatics and phylogenetics.

Index

Converters:

• fasta2phylip.py

  Convert FASTA file to nicely aligned Phylip file.

• phylip2fasta.py

  Convert Phylip file to FASTA file.

Data Processing

• plant_specimen_xlsx_expansion

  Expand plant specimen record lines to corresponding copy numbers for specimen label printing.

Dictionary:

• CSV_Dictionary

  Query multiple lines by first column values in CSV file.

Haplotype Related:

• change_fdi_file_color

  Script to change color, propertion of sector, or maximum node size of fdi file which can be opened Network software.

  Needed txt files (please see example files in txt_files folder) from DNASP and original fdi files (without color information, see fdi_files folder).

• modify_fdi_file_color_with_given_data

  Script to modify color, proportion of sector, and max node size of fdi file with given proportion data (see frequency.raw.txt) and fdi file (see 1.fdi).

• Fdi Generator

  WARNING: FdiGenerator was moved to a standalone repository: FdiGenerator. Please to to this new repository for latest version of FdiGenerator.

  A GUI tool for quickly generating new fdi files with different proportions and colors.

Molecular_Computation

• multiprocessing_jdock

  多进程使用JDOCK运算分子 docking 的脚本。

PCA:

• Randomly_select_and_do_multiple_PCAs

  Randomly select data (similar to bootstrap method) and do PCA, draw PCA plots.

• PCA_with_name

  Do PCA and draw PCA plots with names.