[Treesoft-treefam] (no subject)

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

hi there,
seems like wrong place to submit the query that i have with treebest  
program but anyways, i will try. i want to use modified version of  
the default species tree obtained by "treebest spec" command.
For that i have included SBIRD species (songbird, zebra finch)  
species in aves class which also includes chick species. somehow when  
inferring orthologs, the program does not seem to recognise the  
_SBIRD species and is ignoring it in the process.

Any help on that is welcome. please.

Cheers

original species tree is :
	((ORYSA*-4530.rice,ARATH*-3702)Magnoliophyta-3398, 
(SCHPO*-4896.S_pombe,YEAST*-4932)Ascomycota-4890,
  ((((((((((((HUMAN*-9606,PANTR*-9598.chimpanzee)Homo/Pan/ 
Gorilla-207598,
             MACMU*-9544.monkey)Catarrhini-9526,
             OTOGA-*30611.galago)Primates-9443,
          ((MOUSE*-10090,RAT*-10116)Murinae-39107,RABIT-9986) 
Glires-314147)Euarchontoglires-314146,
         ((BOVIN*-9913.cow,PIG-*9823)Cetartiodactyla-91561,
          (CANFA*-9615.dog,FELCA-*9685.cat)Carnivora-33554,
          SORAR-*42254.shrew,
          MYOLU-*59463.bat)Laurasiatheria-314145,
         (ECHTE-9371.tenrec,LOXAF-9785.elephant)Afrotheria-311790,
         DASNO-9361.armadillo)Eutheria-9347,MONDO*-13616.opossum) 
Theria-32525,
        ORNAN-*9258.platypus)Mammalia-40674,
       CHICK*-9031)Amniota-32524,
      XENTR*-8364.frog)Tetrapoda-32523,
     (BRARE*-7955.zebrafish,
      ((TETNG*-99883.pufferfish,FUGRU*-31033.pufferfish) 
Tetraodontidae-31031,
       (GASAC*-69293.stickleback,ORYLA*-8090.ricefish) 
Smegmamorpha-129949)Percomorpha-32485)Clupeocephala-186625) 
Euteleostomi-117571,
    (CIOIN*-7719,CIOSA*-51511)Ciona-7718)Chordata-7711,
   (((DROME*-7227.fly,DROPS*-7237.fly)Sophophora-32341,
     (AEDAE*-7159.mosquito,ANOGA*-7165.mosquito)Culicidae-7157) 
Diptera-7147,
    APIME-*7460.honeybee)Endopterygota-33392,
   SCHMA*-6183.fluke,
   (CAEEL*-6239.worm,CAEBR*-6238.worm,CAERE*-31234.worm) 
Caenorhabditis-6237)Bilateria-33213)Eukaryota-2759;

----------------------------------------------------
modified species tree including SBIRD is :

((ORYSA*-4530.rice,ARATH*-3702)Magnoliophyta-3398, 
(SCHPO*-4896.S_pombe,YEAST*-4932)Ascomycota-4890,
  ((((((((((((HUMAN*-9606,PANTR*-9598.chimpanzee)Homo/Pan/ 
Gorilla-207598,
             MACMU*-9544.monkey)Catarrhini-9526,
             OTOGA-*30611.galago)Primates-9443,
          ((MOUSE*-10090,RAT*-10116)Murinae-39107,RABIT-9986) 
Glires-314147)Euarchontoglires-314146,
         ((BOVIN*-9913.cow,PIG-*9823)Cetartiodactyla-91561,
          (CANFA*-9615.dog,FELCA-*9685.cat)Carnivora-33554,
          SORAR-*42254.shrew,
          MYOLU-*59463.bat)Laurasiatheria-314145,
         (ECHTE-9371.tenrec,LOXAF-9785.elephant)Afrotheria-311790,
         DASNO-9361.armadillo)Eutheria-9347,MONDO*-13616.opossum) 
Theria-32525,
        ORNAN-*9258.platypus)Mammalia-40674,
       (CHICK*-9031,SBIRD)Aves)Amniota-32524,
      XENTR*-8364.frog)Tetrapoda-32523,
     (BRARE*-7955.zebrafish,
      ((TETNG*-99883.pufferfish,FUGRU*-31033.pufferfish) 
Tetraodontidae-31031,
       (GASAC*-69293.stickleback,ORYLA*-8090.ricefish) 
Smegmamorpha-129949)Percomorpha-32485)Clupeocephala-186625) 
Euteleostomi-117571,
    (CIOIN*-7719,CIOSA*-51511)Ciona-7718)Chordata-7711,
   (((DROME*-7227.fly,DROPS*-7237.fly)Sophophora-32341,
     (AEDAE*-7159.mosquito,ANOGA*-7165.mosquito)Culicidae-7157) 
Diptera-7147,
    APIME-*7460.honeybee)Endopterygota-33392,
   SCHMA*-6183.fluke,
   (CAEEL*-6239.worm,CAEBR*-6238.worm,CAERE*-31234.worm) 
Caenorhabditis-6237)Bilateria-33213)Eukaryota-2759;
--------------------------------------------------------------
the difference is highlighted in both trees.
i have also made sure that the header line alignment is correctly  
correlating with the requirements of inference of species.
cheers

Hardip Patel
CGG, Research School of Biological Sciences
The Australian National University
Acton-2601, Australia