言語系統樹と雑煮の祖先形質復元(kashiwa.r #2)
TRANSCRIPT
解析用ソフトウェア
•系統樹作成
•MrBayes, RAxML, Phylip...
• 祖先形質復元
•Mesquite, BayesTraits...
Rでもできる?本当は「それRでもできるよ!」って書きたかった...
2012年3月3日土曜日
雑煮の進化パターンを探る!
全国お雑煮文化圏地図http://tg.tripadvisor.jp/Zouni/
2012年3月3日土曜日
library("ape")
prefecture<-c("Hokkaido","Aomori","Iwate","Miyage","Akita","Yamagata","Fukushima","Ibaraki","Tochigi","Gunnma","Saitama","Chiba","Tokyo","Kanagawa","Nigata","Toyama","Ishikawa","Fukui","Yamanashi","Nagano","Gifu","Shizuoka","Aichi","Mie","Shiga","Kyoto","Osaka","Hyogo","Nara","Wakayama","Tottori","Shimane","Okayama","Hiroshima","Yamaguchi","Tokushima","Kagawa","Ehime","Kochi","Fukuoka","Saga","Nagasaki","Kumamoto","Oita","Miyazaki","Kagoshima")
dat<-matrix(scan("data.txt",sep=","),nrow=563,ncol=46)dat<-t(dat)rownames(dat)<-prefecturedat.d<-dist.gene(dat)dat.nj<-bionj(dat.d)plot(dat.nj)
2012年3月3日土曜日
library("ape")
prefecture<-c("Hokkaido","Aomori","Iwate","Miyage","Akita","Yamagata","Fukushima","Ibaraki","Tochigi","Gunnma","Saitama","Chiba","Tokyo","Kanagawa","Nigata","Toyama","Ishikawa","Fukui","Yamanashi","Nagano","Gifu","Shizuoka","Aichi","Mie","Shiga","Kyoto","Osaka","Hyogo","Nara","Wakayama","Tottori","Shimane","Okayama","Hiroshima","Yamaguchi","Tokushima","Kagawa","Ehime","Kochi","Fukuoka","Saga","Nagasaki","Kumamoto","Oita","Miyazaki","Kagoshima")
dat<-matrix(scan("data.txt",sep=","),nrow=563,ncol=46)dat<-t(dat)rownames(dat)<-prefecturedat.d<-dist.gene(dat)dat.nj<-bionj(dat.d)plot(dat.nj)
NJ法で系統樹を作成
2012年3月3日土曜日
http://mesquiteproject.org/mesquite/mesquite.html
2012年3月3日土曜日
BayesTraits
http://www.evolution.rdg.ac.uk/BayesTraits.html
2012年3月3日土曜日
角・焼 角・煮
丸・焼 丸・煮
0.021
0.003
0.171
0.036
0.000 0.018 0.016 0.004「丸・焼」型か「丸・煮」型が祖先形質である可能性が高い
2012年3月3日土曜日