From: cmzmasek@gmail.com Date: Wed, 9 Jul 2014 18:35:23 +0000 (+0000) Subject: CYAPA added X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=194abf42b2dd9a45954ee5b0f73e95ff61e85412;p=jalview.git CYAPA added --- diff --git a/forester/data/surfacing/genome_locations.txt b/forester/data/surfacing/genome_locations.txt index 93df656..9faab1d 100644 --- a/forester/data/surfacing/genome_locations.txt +++ b/forester/data/surfacing/genome_locations.txt @@ -1,4 +1,4 @@ -# Last updated: 140708 +# Last updated: 140709 # # Ophistokonta::Animals (mammals) BOVIN /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/BOVIN.fasta @@ -208,7 +208,7 @@ ENTBH /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/E ENTDS /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ENTDS.fasta ENTHI /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ENTHI.fasta POLPA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/POLPA.fasta -# Archaeplastida::Viridaeplantae::Streptophyta +# Viridaeplantae::Streptophyta AMBTC /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AMBTC.fasta AQUCA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AQUCA.fasta ARALY /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ARALY.fasta @@ -240,7 +240,7 @@ SORBI /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/S SOYBN /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/SOYBN.fasta THEHA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/THEHA.fasta VITVI /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/VITVI.fasta -# Archaeplastida::Viridaeplantae::Chlorophyta +# Viridaeplantae::Chlorophyta ASCXX /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ASCXX.fasta CHLRE /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CHLRE.fasta CHLVA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CHLVA.fasta @@ -251,8 +251,10 @@ ORCXX /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/O OSTLU /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/OSTLU.fasta OSTTA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/OSTTA.fasta VOLCA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/VOLCA.fasta -# Archaeplastida::Rhodophyta +# Rhodophyta CYAME /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CYAME.fasta +# Glaucophyta +CYAPA /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CYAPA.fasta # Chromalveolates AKEXX /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AKEXX.fasta ALIXX /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ALIXX.fasta diff --git a/forester/data/surfacing/genome_locations_eos.txt b/forester/data/surfacing/genome_locations_eos.txt index 7eb9f45..cc3bf20 100644 --- a/forester/data/surfacing/genome_locations_eos.txt +++ b/forester/data/surfacing/genome_locations_eos.txt @@ -1,4 +1,4 @@ -# Last updated: 140708 +# Last updated: 140709 # # Ophistokonta::Animals (mammals) BOVIN /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/BOVIN.fasta @@ -208,7 +208,7 @@ ENTBH /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTBH.fasta ENTDS /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTDS.fasta ENTHI /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTHI.fasta POLPA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/POLPA.fasta -# Archaeplastida::Viridaeplantae::Streptophyta +# Viridaeplantae::Streptophyta AMBTC /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AMBTC.fasta AQUCA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AQUCA.fasta ARALY /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ARALY.fasta @@ -240,7 +240,7 @@ SORBI /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/SORBI.fasta SOYBN /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/SOYBN.fasta THEHA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/THEHA.fasta VITVI /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/VITVI.fasta -# Archaeplastida::Viridaeplantae::Chlorophyta +# Viridaeplantae::Chlorophyta ASCXX /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ASCXX.fasta CHLRE /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CHLRE.fasta CHLVA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CHLVA.fasta @@ -251,8 +251,10 @@ ORCXX /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ORCXX.fasta OSTLU /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/OSTLU.fasta OSTTA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/OSTTA.fasta VOLCA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/VOLCA.fasta -# Archaeplastida::Rhodophyta +# Rhodophyta CYAME /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CYAME.fasta +# Glaucophyta +CYAPA /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CYAPA.fasta # Chromalveolates AKEXX /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AKEXX.fasta ALIXX /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ALIXX.fasta diff --git a/forester/data/surfacing/genomes_all.txt b/forester/data/surfacing/genomes_all.txt index 2539986..d479c76 100644 --- a/forester/data/surfacing/genomes_all.txt +++ b/forester/data/surfacing/genomes_all.txt @@ -1,4 +1,4 @@ -# Last updated: 140708 +# Last updated: 140709 # # Ophistokonta::Animals (mammals) /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOVIN.hmmscan BOVIN @@ -204,7 +204,7 @@ /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 -# 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 @@ -236,7 +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 -# 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 @@ -247,8 +247,10 @@ /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 -# Archaeplastida::Rhodophyta +# Rhodophyta /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAME.hmmscan CYAME +# 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 diff --git a/forester/data/surfacing/genomes_eos_all.txt b/forester/data/surfacing/genomes_eos_all.txt index 9cad5d5..e9ef1dd 100644 --- a/forester/data/surfacing/genomes_eos_all.txt +++ b/forester/data/surfacing/genomes_eos_all.txt @@ -1,4 +1,4 @@ -# Last updated: 140708 +# Last updated: 140709 # # Ophistokonta::Animals (mammals) /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOVIN.hmmscan BOVIN @@ -204,7 +204,7 @@ /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTDS.hmmscan ENTDS /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTHI.hmmscan ENTHI /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/POLPA.hmmscan POLPA -# Archaeplastida::Viridaeplantae::Streptophyta +# Viridaeplantae::Streptophyta /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AMBTC.hmmscan AMBTC /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AQUCA.hmmscan AQUCA /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARALY.hmmscan ARALY @@ -236,7 +236,7 @@ /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SOYBN.hmmscan SOYBN /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEHA.hmmscan THEHA /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VITVI.hmmscan VITVI -# Archaeplastida::Viridaeplantae::Chlorophyta +# Viridaeplantae::Chlorophyta /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ASCXX.hmmscan ASCXX /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLRE.hmmscan CHLRE /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLVA.hmmscan CHLVA @@ -247,8 +247,10 @@ /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTLU.hmmscan OSTLU /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTTA.hmmscan OSTTA /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VOLCA.hmmscan VOLCA -# Archaeplastida::Rhodophyta +# Rhodophyta /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAME.hmmscan CYAME +# Glaucophyta +/home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAPA.hmmscan CYAPA # Chromalveolates /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AKEXX.hmmscan AKEXX /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ALIXX.hmmscan ALIXX diff --git a/forester/data/tol_156.xml b/forester/data/tol_156.xml index 8768717..80141c2 100644 --- a/forester/data/tol_156.xml +++ b/forester/data/tol_156.xml @@ -5153,7 +5153,6 @@ 38254 Glaucocystophyceae - Glaucophyta class @@ -5184,7 +5183,8 @@ Emiliania huxleyi Pontosphaera huxleyi species - http://research.kahaku.go.jp/zoology/kaisei/hp-2/images/hapto.jpg + http://www.nhm.ac.uk/resources-rx/images/1049/emiliania-huxleyi-light-microscope-image_68318_1.jpg + http://cmore.soest.hawaii.edu/education/kidskorner/images/emiliania_600px.jpg