Phylogenetics in R: collapsing descendant tips of an internal node -


i have several thousand gene trees trying ready analysis codeml. tree below typical example. want automate collapsing of tips or nodes appear duplicates. instance, descendants of node 56 tips 26, 27, 28 etc way 36. of these other tip 26 appear duplicates. how can collapse them single tip, leaving tips 28 , 1 representative of other tips descendants of node 56?

i know how manually 1 one, trying automate process function can identify tips need collapsed , reduce them single representative tip. far have been looking @ cophenetic function calculates distances between tips. however, not sure how use information collapse tips.

here newick string below tree:

((((11:0.00201426,12:5e-08,(9:1e-08,10:1e-08,8:1e-08)40:0.00403036)41:0.00099978,7:5e-08)42:0.01717066,(3:0.00191517,(4:0.00196859,(5:1e-08,6:1e-08)71:0.00205168)70:0.00112995)69:0.01796015)43:0.042592645,((1:0.00136179,2:0.00267375)44:0.05586907,(((13:0.00093161,14:0.00532243)47:0.01252989,((15:1e-08,16:1e-08)49:0.00123243,(17:0.00272478,(18:0.00085725,19:0.00113572)51:0.01307761)50:0.00847373)48:0.01103656)46:0.00843782,((20:0.0020268,(21:0.00099593,22:1e-08)54:0.00099081)53:0.00297097,(23:0.00200672,(25:1e-08,(36:1e-08,37:1e-08,35:1e-08,34:1e-08,33:1e-08,32:1e-08,31:1e-08,30:1e-08,29:1e-08,28:0.00099682,27:1e-08,26:1e-08)58:0.00200056,24:1e-08)56:0.00100953)55:0.00210137)52:0.01233888)45:0.01906982)73:0.003562205)38;

enter image description here

one option drop tips have length beneath threshold.

drop_dupes <- function(tree,thres=1e-5){   tips <- which(tree$edge[,2] %in% 1:ntip(tree))   todrop <- tree$edge.length[tips] < thres   drop.tip(tree,tree$tip.label[todrop]) }  plot(drop_dupes(tree))

enter image description here


Comments

Post a Comment

Popular posts from this blog

jOOQ update returning clause with Oracle -

according http://www.jooq.org/doc/3.8/manual/sql-building/sql-statements/update-statement/ jooq doesn't support returning clause in update statements databases except firebird , postgres. does know, still correct oracle jooq? according oracle's documentation, oracle db supports returning clase delete, insert, or update statements. incorrect manual you're right - manual wrong , should fixed: https://github.com/jooq/jooq/issues/5470 single row update returning jooq 3.8 added support single row update .. returning statements. internally, uses callablestatement , pl/sql block of form: begin update "my_table" set "my_table"."column" = 'xyz' "my_table"."id" = 1 returning "my_table"."id", "my_table"."column" ?, ?; ? := sql%rowcount; end; the relevant issue is: https://github.com/jooq/jooq/issues/5190 multi row update returning a...
Read more

java - Warning equals/hashCode on @Data annotation lombok with inheritance -

i have entity inherits other. on other hand, i'm using lombok project reduce boilerplate code, put @data annotation. annotation @data inheritance produces next warning: generating equals/hashcode implementation without call superclass, though class not extend java.lang.object. if intentional, add '@equalsandhashcode(callsuper=false)' type. is advisable add annotation @equalsandhashcode (callsuper = true) or @equalsandhashcode (callsuper = false) ? if not added, 1 callsuper=false or callsuper=true ? the default value false . 1 if don't specify , ignore warning. yes, recommended add @equalsandhashcode annotation on @data annotated classes extend else object. cannot tell if need true or false , depends on class hierarchy, , need examined on case-by-case basis. however, project or package, can configure in lombok.config call super methods if not direct subclass of object. lombok.equalsandhashcode.callsuper = call for configuration system ...
Read more

java - BasicPathUsageException: Cannot join to attribute of basic type -

i using java 8 jpa (hibernate 5.2.1). have clause works perfectly, until introduce clause make use foreign key table values too. i getting following error: basicpathusageexception: cannot join attribute of basic type i think problem related fact have join table, , not sure how create join using join table. employee - employee_category - category model (employee.java): @manytomany(cascade = cascadetype.all, fetch=fetchtype.eager) @jointable ( name="employee_category", joincolumns={ @joincolumn(name="emp_id", referencedcolumnname="id") }, inversejoincolumns={ @joincolumn(name="cat_id", referencedcolumnname="id") } ) private set<category> categories; model (category.java): @id private string id; jpa when introduce following code, fails error above (i think problem new piece of code): join<t, category> category = from.join("id"); predicates.add(criteriabuilder.like(category....
Read more