PyPedal - BioHackersNet

Python으로 씌여진 Pedigree 분석 프로그램

http://pypedal.sourceforge.net/

혈통정보를 입력받아, 다양한 혈통관련 통계계산들을 수행하고, 계산 결과를 차트로 표시하거나, 가계도를 그려준다. PyPedal has been used to perform calculations on pedigrees as large as 600,000 animals and has been used in scientific research (Cole, Franke, and Leighton 2004; Cole 2007).

주요기능

Reading pedigree files in user-defined formats; 사용자정의 포맷으로 가계도 데이터 입력가능
Checking pedigree integrity (duplicate IDs, parents younger than offspring, etc.); 가계정보 체크기능
Generating summary information such as frequency of appearance in the pedigree file; 가계정보 요약기능
Reordering and renumbering of pedigree files. : 가계정보 재정렬 기능
Computation of the numerator relationship matrix (A) from a pedigree file using the tabular method; 가계 행렬 계산 기능
Inbreeding calculations for large pedigrees; 대형 가계를 위한 육종관련 계산 기능
Computation of average total and average individual coefficients of inbreeding and relationship; 육종관련 통계수치 계산 기능
Calculation of coefficients of partial inbreeding using an iterative tabulat method ( Lacy, Alaks, and Walsh 1996; Gulisija, Gianola, Weigel, and Toro 2006); iterative tabulat method를 이용한 partial inbreeding coefficients 계산기능
Calculation of coefficients of ancestral inbreeding using the methods of Ballou ( 1997) or Suwanlee et al. (2007); Ballou method 를 이용한 ancestral inbreeding coefficient 계산 기능
Decomposition of A into T and D such that A = T DT ;
Computation of the direct inverse of A (not accounting for inbreeding) using the method of Henderson ( 1976);
Computation of the direct inverse of A (accounting for inbreeding) using the method of Quaas ( 1976);
Storage of A and its inverse between user sessions as persistent Python objects using the pickle module to avoid unnecessary calculations;
Calculation of theoretical and actual effective population sizes;
Computation of effective founder number using the exact algorithm of Lacy ( 1989);
Computation of effective founder number using the approximate algorithm of Boichard et al. ( 1997);
Computation of effective ancestor number using the algorithms of Boichard et al. ( 1997);
Selection of subpedigrees containing all ancestors of an animal;
Identification of the common relatives of two animals;
Calculation of the inbreeding of offspring from a prospective mating;
Output to ASCII text files, including matrices, coefficients of inbreeding and relationship, and summary information;
Importation and exportation of GEDCOM 5.5 files;
Loading pedigrees from, and saving them to, MySQL, Postgres, and SQLite databases;
Simulation of pedigrees using an algorithm derived from that in Matvec 1.1a;

아래와 같은 확장이 필요하다.

(위 확장에서 볼수 있듯이, 다양한 네트워크 다이어그램들을 보여주는듯.)