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[jalview.git] / forester / data / surfacing / genomes_all.txt
diff --git a/forester/data/surfacing/genomes_all.txt b/forester/data/surfacing/genomes_all.txt
index 2be43f8..d479c76 100644 (file)
--- a/forester/data/surfacing/genomes_all.txt
+++ b/forester/data/surfacing/genomes_all.txt
@@ -1,3 +1,5 @@
+# Last updated: 140709
+#
 # Ophistokonta::Animals (mammals)
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOVIN.hmmscan    BOVIN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CANFA.hmmscan    CANFA
@@ -15,18 +17,20 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ORNAN.hmmscan    ORNAN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OTOGA.hmmscan    OTOGA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PANTR.hmmscan    PANTR
-/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PIG.hmmscan    PIG
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PIG.hmmscan      PIG
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RABIT.hmmscan    RABIT
-/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RAT.hmmscan    RAT
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RAT.hmmscan      RAT
 # Ophistokonta::Animals (except mammals)
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ACRDI.hmmscan    ACRDI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ACREC.hmmscan    ACREC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ACYPI.hmmscan    ACYPI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AEDAE.hmmscan    AEDAE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AMPQE.hmmscan    AMPQE
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ANAPL.hmmscan    ANAPL
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ANOCA.hmmscan    ANOCA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ANOGA.hmmscan    ANOGA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/APIME.hmmscan    APIME
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ASTMX.hmmscan    ASTMX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ATTCE.hmmscan    ATTCE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOMMO.hmmscan    BOMMO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BRAFL.hmmscan    BRAFL
@@ -36,13 +40,14 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CAEEL.hmmscan    CAEEL
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CAEJA.hmmscan    CAEJA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CAERE.hmmscan    CAERE
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CALMI.hmmscan    CALMI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CAMFO.hmmscan    CAMFO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHICK.hmmscan    CHICK
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CIOIN.hmmscan    CIOIN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CIOSA.hmmscan    CIOSA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CLOSI.hmmscan    CLOSI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CRAGI.hmmscan    CRAGI
-/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CTEXX.hmmscan    CTEXX
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CAPTE.hmmscan    CAPTE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CULPI.hmmscan    CULPI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/DANPL.hmmscan    DANPL
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/DANRE.hmmscan    DANRE
@@ -60,20 +65,26 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/DROWI.hmmscan    DROWI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/DROYA.hmmscan    DROYA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ECHMU.hmmscan    ECHMU
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/FICAL.hmmscan    FICAL
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/GADMO.hmmscan    GADMO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/GASAC.hmmscan    GASAC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/HELRO.hmmscan    HELRO
-/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/HMAXX.hmmscan    HMAXX
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/HYDVU.hmmscan    HYDVU
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/HYMMI.hmmscan    HYMMI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/IXOSC.hmmscan    IXOSC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/LATCH.hmmscan    LATCH
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/LEPOC.hmmscan    LEPOC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/LOTGI.hmmscan    LOTGI
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/LYTVA.hmmscan    LYTVA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MELGA.hmmscan    MELGA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MNELE.hmmscan    MNELE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/NASVI.hmmscan    NASVI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/NEMVE.hmmscan    NEMVE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OIKDI.hmmscan    OIKDI
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OPHHA.hmmscan    OPHHA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ORENI.hmmscan    ORENI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ORYLA.hmmscan    ORYLA
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PATMI.hmmscan    PATMI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PEDHC.hmmscan    PEDHC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PELSI.hmmscan    PELSI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PETMA.hmmscan    PETMA
@@ -140,7 +151,7 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MAGGR.hmmscan    MAGGR
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MALGO.hmmscan    MALGO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MELLP.hmmscan    MELLP
-/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MPSXX.hmmscan    MPSXX
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SPHMS.hmmscan    SPHMS
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MUCCI.hmmscan    MUCCI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MVNXX.hmmscan    MVNXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/MYCGM.hmmscan    MYCGM
@@ -156,6 +167,8 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PPLXX.hmmscan    PPLXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PUCGR.hmmscan    PUCGR
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PYRTR.hmmscan    PYRTR
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RHIID.hmmscan    RHIID
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RHIO9.hmmscan    RHIO9
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RHIOR.hmmscan    RHIOR
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RHOGR.hmmscan    RHOGR
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SCHJY.hmmscan    SCHJY
@@ -191,7 +204,8 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTDS.hmmscan    ENTDS
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTHI.hmmscan    ENTHI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/POLPA.hmmscan    POLPA
-# Corticata::Archaeplastida::Viridaeplantae::Streptophyta
+# Viridaeplantae::Streptophyta
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AMBTC.hmmscan    AMBTC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AQUCA.hmmscan    AQUCA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARALY.hmmscan    ARALY
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARATH.hmmscan    ARATH
@@ -222,7 +236,7 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SOYBN.hmmscan    SOYBN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEHA.hmmscan    THEHA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VITVI.hmmscan    VITVI
-# Corticata::Archaeplastida::Viridaeplantae::Chlorophyta
+# Viridaeplantae::Chlorophyta
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ASCXX.hmmscan    ASCXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLRE.hmmscan    CHLRE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLVA.hmmscan    CHLVA
@@ -233,9 +247,11 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTLU.hmmscan    OSTLU
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTTA.hmmscan    OSTTA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VOLCA.hmmscan    VOLCA
-# Corticata::Archaeplastida::Rhodophyta
+# Rhodophyta
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAME.hmmscan    CYAME
-# Corticata::Chromalveolates
+# Glaucophyta
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAPA.hmmscan    CYAPA
+# Chromalveolates
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AKEXX.hmmscan    AKEXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ALIXX.hmmscan    ALIXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AURAN.hmmscan    AURAN
@@ -243,6 +259,9 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BLAHO.hmmscan    BLAHO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CRYHO.hmmscan    CRYHO
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CRYPI.hmmscan    CRYPI
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/EIMAC.hmmscan    EIMAC
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ICHMG.hmmscan    ICHMG
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/PERM5.hmmscan    PERM5
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ECTSI.hmmscan    ECTSI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/EMIHU.hmmscan    EMIHU
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/FCYXX.hmmscan    FCYXX
@@ -266,7 +285,7 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEAN.hmmscan    THEAN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEPA.hmmscan    THEPA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/TOXGO.hmmscan    TOXGO
-# Cabozoa::Excavata
+# Excavata
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BODSA.hmmscan    BODSA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/GIAIC.hmmscan    GIAIC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/LEIBR.hmmscan    LEIBR
@@ -275,8 +294,9 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/NAEGR.hmmscan    NAEGR
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/TRIVA.hmmscan    TRIVA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/TRYB2.hmmscan    TRYB2
-# Cabozoa::Rhizaria
+# Rhizaria
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BIGNA.hmmscan    BIGNA
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/RETFI.hmmscan    RETFI
 # Archaea
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AERPE.hmmscan    AERPE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARCFU.hmmscan    ARCFU