Hello everyone; When I use codeml in pamlX , the program dont read the unrooted tree, but when i use a tree which, is reconstracted with MEGA6 the program runs. whats the problem? Is anything is wrong with this tree?
((((HVU0037G3443:0.05248305870066112,BRADI1G23510:0.0367431526985914):0.02477484259328695,LOCOS07G39270:0.08554672069239334):0.0517894133870083,SEITA2G368100:0.0363710136011255):0.0292925973936597,(((((HVU0041G2553:0.1256677960765632,HVU0041G3380:0.09897251356397156):0.1346398815049772,((BRADI2G08730:0.1347896694997399,(SEITA5G062900:0.07694365593931043,(SOBIC003G111500:0.04009375379685257,ZM00001D008370:0.05116603471101672):0.04343334725700698):0.156985663612545):0.03314864183286258,LOCOS01G14630:0.1325123314021834):0.07697359173280986):0.2529331573752677,(BRADI3G51245:0.08775617585217899,(LOCOS02G44780:0.07001349051066684,(SEITA1G266500:0.02887454891053994,(SOBIC004G287300:0.0141941477000682,(ZM00001D017540:0.0399622162918856,ZM00001D051416:0.02500790169156237):0.01340701865126353):0.03096138170412624):0.02804638054499954):0):1.52032125047148):0.4953016936251166,ZM00001D006678:0):0.05084891100249466,ZM00001D021929:0.04704206688817056):0.03207914363316525,SOBIC002G353300:0.008540475270662293):0;
I used model=0 and NSsites= 0 clock=1 codon freq=2
The software gives this message at the end Species BRADI1G23510?
the MEGA6 tree is: ((((((Zm00001d006678:0.04957551,Zm00001d021929:0.04547446):0.03606685,Sobic.002G353300:0.01106735):0.03286665,Seita.2G368100:0.03637959):0.01084911,(LOCOs07g39270:0.09587520,(HVU0037G3443:0.05368905,Bradi1g23510:0.04562513):0.02711137):0.04746501):0.52711352,(((HVU0041G2553:0.12145118,HVU0041G3380:0.09829999):0.14963258,Bradi2g08730:0.11322183):0.02293290,(LOCOs01g14630:0.10782857,(Seita.5G062900:0.06756550,(Sobic.003G111500:0.04219704,Zm00001d008370:0.04839744):0.04221195):0.11011175):0.01583605):0.21614442):0.34258946,((Bradi3g51245:0.07466861,LOCOs02g44780:0.06153694):0.01457478,(Seita.1G266500:0.02250546,(Sobic.004G287300:0.01474354,(Zm00001d017540:0.03854642,Zm00001d051416:0.02343852):0.01043782):0.02902462):0.00712552):0.92379980);
I get the same error. This was posted here a while ago. Have you since worked out what was going on?