2008-05-16
org.kosen.entty.User@345e1112
오용식(rockeryosi)
- 1
PAUP 4.0 beta10 프로그램을 이용해서
phylogenetic tree 중 maximum parsimony을 그리려하는데,,
NOTE에 이러한 내용이 나오던군요,,
Character-status summary:
Current optimality criterion = parsimony
No characters are excluded
Of 1385 total characters:
All characters are of type 'unord'
All characters have equal weight
1004 characters are constant
211 variable characters are parsimony-uninformative
Number of parsimony-informative characters = 170
No trees in memory; “SaveTrees“ command ignored.
Heuristic search settings:
Optimality criterion = parsimony
Character-status summary:
Of 1385 total characters:
All characters are of type 'unord'
All characters have equal weight
1004 characters are constant
211 variable characters are parsimony-uninformative
Number of parsimony-informative characters = 170
Gaps are treated as “missing“
Multistate taxa interpreted as uncertainty
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 10
Starting seed = 1033027247
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR)
Steepest descent option not in effect
Initial 'MaxTrees' setting = 100
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
Topological constraints not enforced
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 37905
Score of best tree(s) found = 825
Number of trees retained = 2
Time used = 0.14 sec
Tree-island profile:
First Last First Times
Island Size tree tree Score replicate hit
----------------------------------------------------------------------
1 2 1 2 825 1 10
이렇게요;;;;;;
이거 정확히 그린거 맞을까요??
PAUP 4.0 프로그램을 처음 사용하고, 주위에도 사용한 사람이 하나도 없어서 어려움이 많네요;;; 도움 부탁드립니다 ^^;;
- phylogenetic tree
지식의 출발은 질문, 모든 지식의 완성은 답변!
각 분야 한인연구자와 현업 전문가분들의 답변을 기다립니다.
각 분야 한인연구자와 현업 전문가분들의 답변을 기다립니다.
답변 1
-
답변
조민석님의 답변
2008-05-29- 0
밑에 나온 내용은 PAUP 설정 메뉴 셋팅값입니다.. 처음에 지정을 어떻게 했는지 알려주는건데.. 옵션에 따라 트리가 조금씩 달라지긴 하지만.. 큰 영향을 줄 정도는 아닙니다.. 다른 알고리즘으로 그릴 경우 ML이나, NJ, BI등을 사용하시면 되구요.. 저걸 논문에 쓸때 표기하기도 하구 안하기도 합니다.. 요즘엔 트리 그릴때는 한개 프로그램만 사용하기 보다는 여러개를 동시에 돌리는 추세입니다.. ^^ >PAUP 4.0 beta10 프로그램을 이용해서 >phylogenetic tree 중 maximum parsimony을 그리려하는데,, >NOTE에 이러한 내용이 나오던군요,, > > >Character-status summary: > Current optimality criterion = parsimony > No characters are excluded > Of 1385 total characters: > All characters are of type 'unord' > All characters have equal weight > 1004 characters are constant > 211 variable characters are parsimony-uninformative > Number of parsimony-informative characters = 170 > >No trees in memory; “SaveTrees“ command ignored. > >Heuristic search settings: > Optimality criterion = parsimony > Character-status summary: > Of 1385 total characters: > All characters are of type 'unord' > All characters have equal weight > 1004 characters are constant > 211 variable characters are parsimony-uninformative > Number of parsimony-informative characters = 170 > Gaps are treated as “missing“ > Multistate taxa interpreted as uncertainty > Starting tree(s) obtained via stepwise addition > Addition sequence: random > Number of replicates = 10 > Starting seed = 1033027247 > Number of trees held at each step during stepwise addition = 1 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Initial 'MaxTrees' setting = 100 > Branches collapsed (creating polytomies) if maximum branch length is zero > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic sea>rch completed > Total number of rearrangements tried = 37905 > Score of best tree(s) found = 825 > Number of trees retained = 2 > Time used = 0.14 sec > >Tree-island profile: > First Last First Times >Island Size tree tree Score replicate hit >---------------------------------------------------------------------- > 1 2 1 2 825 1 10 > > > >이렇게요;;;;;; >이거 정확히 그린거 맞을까요?? >PAUP 4.0 프로그램을 처음 사용하고, 주위에도 사용한 사람이 하나도 없어서 어려움이 많네요;;; 도움 부탁드립니다 ^^;;