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data/outgroup_eval_only/NCBI/Anidulans/GCF_000011425.1_ASM1142v1_genomic.fna.gz

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data/outgroup_eval_only/NCBI/Anidulans/GCF_000011425.1_ASM1142v1_genomic.gff.gz

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data/outgroup_eval_only/NCBI/Drerio/GCF_049306965.1_GRCz12tu_genomic.fna.gz

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data/outgroup_eval_only/NCBI/Drerio/GCF_049306965.1_GRCz12tu_genomic.gff.gz

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data/outgroup_eval_only/Phytozome/Download_1986148_File_Manifest.csv

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+"filename","file_id","JGI Grouping ID","directory/path","Short Organism Name","Genome/Metagenome Name","md5 checksum","file size"
+"Slycopersicum_796_ITAG5.0.repeatmasked_assembly_SL5.0.gff3.gz","64090959b335b1a5dc9267c8","Phytozome-796","Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0/annotation","Slycopersicum","Solanum lycopersicum ITAG5.0","4aca21a234c505edc5b4ba788f454616","32761763"
+"Slycopersicum_796_SL5.0.softmasked.fa.gz","6409095ab335b1a5dc9267d7","Phytozome-796","Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0/assembly","Slycopersicum","Solanum lycopersicum ITAG5.0","ec5f022413d458627a8ffbaaa6b9d8b6","250716875"
+"Slycopersicum_796_ITAG5.0.readme.txt","64090959b335b1a5dc9267c5","Phytozome-796","Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0","Slycopersicum","Solanum lycopersicum ITAG5.0","0a7571ad3252940ad4135602d508d1a8","5671"
+"Ppatens_947_v7.1.readme.txt","69e07f9c700f9528bee6a040","Phytozome-947","Phytozome/PhytozomeV14/Ppatens/v7.1/assembly","Ppatens","Phytozome-947","6cb79e2bd9ef4228eb033dc57046f6ef","5125"
+"Ppatens_947_v7.1.gene.gff3.gz","684a1e1389cc9f214d4ccc9b","Phytozome-947","Phytozome/PhytozomeV14/Ppatens/v7.1/annotation","Ppatens","Phytozome-947","7ca87085581f3d888c001acf5ddb43a1","40320675"
+"Ppatens_947_v7.1.fa.gz","6960265687a5a856eba6ba2c","Phytozome-947","Phytozome/PhytozomeV14/Ppatens/v7.1/assembly","Ppatens","Phytozome-947","b031303ddd67ad29283b0a0e35fedfe6","144800525"

data/outgroup_eval_only/Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0/Slycopersicum_796_ITAG5.0.readme.txt

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+A standard set of annotation and assembly files released as part of Phytozome release.
+
+Organism = Solanum lycopersicum
+NCBI-Taxonomy-ID = 4081
+Assembly-version = SL5.0
+Annotation-version = ITAG5.0
+
+All FASTA and GFF3 files are compressed by gzip to reduce the file size for faster downloads.
+Note: the number 796 in all file names is a Phytozome internal identifier for the current release of this genome annotation
+      and can be safely ignored.
+
+Notes on JGI locus/gene naming convention: starting in 2013, JGI plant genome group began to use following naming pattern: 
+   a) Prefix.NGn for stable chromosome scale genome assembly, example: Glyma.01G000100;
+   b) Prefix.Zn for chromosome scale genome assembly, example: Eucgr.A00001, Pavir.Aa00001;
+   c) Prefix.Nsn for fragmented genome assembly, example: Pahal.0001s0001
+where N is chromosome number in a) or scaffold/contig number in c), Z is a letter representing a chromosome number like A for 1, B for 2 and so on in b), and n is locus/gene number on a chromosome or scaffold/contig. In both a) and b), a letter after last chromosome represents all scaffold/contig that are not mapped to a chromosome, for example, Glyma.U045300 (soybean has 20 chromosomes, 21st alphabet is U). Polyploid genome chromosome number can have a letter representing subgenome and hence N and Z could have one more letter like Pavir.Aa00001. Digit width of N in a) is variable ranging from 1 to 3, dot (period) is optional, and Prefix is made up from organism genus and species or chosen by community. Transcript name is locus name plus . plus digits (transcript number digit), for example, Glyma.01G000100.1. Initially transcript having digit 1 is longest but in subsequent gene annotation, transcript with digit 1 can be lost or not longest any more. The longest transcript should be looked up from GFF3 file with attribute longest=1. Initially, locus/gene number is ordered and increased by 100 from chromosome left to right in a), but this is very likely to change when genome assembly and/or gene annotation is updated. Please refer to external source for naming pattern for third party gene sets in Phytozome.
+
+Files in the annotation subdirectory:
+1) Slycopersicum_796_ITAG5.0.annotation_info.txt
+   A summary of annotation details available in Phytozome. This is a tab-delimited file, as follows:
+   (Note: Columns are blank if no corresponding data is available)
+   1: Phytozome internal transcript ID (potentially useful to connect to biomart datasets)
+   2: Phytozome gene locus name
+   3: Phytozome transcript name
+   4: Phytozome protein name (often same as transcript name, but this can vary)
+   5: PFAM
+   6: Panther
+   7: KOG
+   8: KEGG ec
+   9: KEGG Orthology
+  10: Gene Ontology terms (NOTE: these are automated results from interpro2go in most genomes, *not* empirically derived)
+  Rest of columns are for best hit (please read file header)
+
+"Best hits" are defined as the top result returned from BLASTP alignment of this species proteome to the target 
+    (A. thaliana, O. sativa, or C. reinhardtii listed above). This was run with blast+ 2.2.26 with parameters:
+    blastall -p blastp -F "mS" -b 1500 -v 1500 -e 0.001 -M BLOSUM45
+    and further filtered with an 1E-3 cutoff e-value.
+"Best hits" can also be obtained fron inparanoid computes against target(s) if not by BLASTP for newer gene set release
+
+2) Slycopersicum_796_ITAG5.0.cds.fa.gz and Slycopersicum_796_ITAG5.0.cds_primaryTranscriptOnly.fa.gz
+   Nucleotide FASTA format file of all gene coding sequences, with or without alternative splice variants
+
+3) Slycopersicum_796_ITAG5.0.protein.fa.gz and Slycopersicum_796_ITAG5.0.protein_primaryTranscriptOnly.fa.gz
+   Amino acid FASTA format file of all gene coding sequences, with or without alternative splice variants
+
+4) Slycopersicum_796_ITAG5.0.transcript.fa.gz and Slycopersicum_796_ITAG5.0.transcript_primaryTranscriptOnly.fa.gz
+   Nucleotide FASTA format file of spliced mRNA transcripts (UTR, exons), with or without alternative splice variants
+
+5) Slycopersicum_796_ITAG5.0.gene.gff3.gz
+   GFF3 format representation of all mRNA sequences (UTR, CDS). Genomic coordinates are relative to the reference 
+   sequence in column 1
+
+6) Slycopersicum_796_ITAG5.0.gene_exons.gff3.gz
+   GFF3 format representation of all mRNA sequences as above, but with exon subfeatures. Genomic coordinates are 
+   relative to the reference sequence in column 1
+
+
+7) Slycopersicum_796_ITAG5.0.defline.txt
+   Tab-delimited list of all defline for the Phytozome transcript in the first column or provisional defLine (pdef type in second column).
+   Provisional deflines (aka auto defline) are generated via an automated method that prioritizes KEGG/EC over Panther over KOG 
+   over PFAM annotations, and then chooses the one with lowest multiplicity (M), where M indicates how many other genes in this genome 
+   have the same annotation.
+
+8) Slycopersicum_796_ITAG5.0.repeatmasked_assembly_SL5.0.gff3.gz
+   repeat GFF, mostly by RepeatMasker, some by MerMasking, still some derived from masked genome fasta
+
+
+-----
+Files in the assembly subdirectory:
+1) Slycopersicum_796_SL5.0.fa.gz
+   Nucleotide FASTA format of the current genomic assembly
+
+2) Slycopersicum_796_SL5.0.softmasked.fa.gz
+   Slycopersicum_796_SL5.0.hardmasked.fa.gz
+   Nucleotide FASTA format of the current genomic assembly, masked for repetitive sequence by RepeatMasker 
+   (softmasked sequence is in lower case; hardmasked replaces masked sequence with Ns).
+
+
+-----
+Files in the additional subdirectories (expression, diversity, etc.) are releases of data related to the current 
+   annotation, and are not always available for all organisms.

data/outgroup_eval_only/Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0/annotation/Slycopersicum_796_ITAG5.0.repeatmasked_assembly_SL5.0.gff3.gz

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+size 32761763

data/outgroup_eval_only/Phytozome/PhytozomeV13/Slycopersicum/ITAG5.0/assembly/Slycopersicum_796_SL5.0.softmasked.fa.gz

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+oid sha256:65d12240c8a2844ae1103f34566809de3b6d9edcb0ea4242dc2625e15366f671
+size 250716875

data/outgroup_eval_only/Phytozome/PhytozomeV14/Ppatens/v7.1/annotation/Ppatens_947_v7.1.gene.gff3.gz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:4d36fe47a57f523ccf6a9a9727b19bbd05cae797d84709cb3a15f102a1372331
+size 40320675

data/outgroup_eval_only/Phytozome/PhytozomeV14/Ppatens/v7.1/assembly/Ppatens_947_v7.1.fa.gz

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+version https://git-lfs.github.com/spec/v1
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+size 144800525

data/outgroup_eval_only/Phytozome/PhytozomeV14/Ppatens/v7.1/assembly/Ppatens_947_v7.1.readme.txt

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+A standard set of annotation and assembly files released as part of Phytozome release.
+
+Organism = Physcomitrium patens
+NCBI-Taxonomy-ID = 3218
+Assembly-version = V7
+Annotation-version = v7.1
+
+All FASTA and GFF3 files are compressed by gzip to reduce the file size for faster downloads.
+Note: the number 947 in all file names is a Phytozome internal identifier for the current release of this genome annotation
+      and can be safely ignored.
+
+Notes on JGI locus/gene naming convention: starting in 2013, JGI plant genome group began to use following naming pattern: 
+   a) Prefix.NGn for stable chromosome scale genome assembly, example: Glyma.01G000100;
+   b) Prefix.Zn for chromosome scale genome assembly, example: Eucgr.A00001, Pavir.Aa00001;
+   c) Prefix.Nsn for fragmented genome assembly, example: Pahal.0001s0001
+where N is chromosome number in a) or scaffold/contig number in c), Z is a letter representing a chromosome number like A for 1, B for 2 and so on in b), and n is locus/gene number on a chromosome or scaffold/contig. In both a) and b), a letter after last chromosome represents all scaffold/contig that are not mapped to a chromosome, for example, Glyma.U045300 (soybean has 20 chromosomes, 21st alphabet is U). Polyploid genome chromosome number can have a letter representing subgenome and hence N and Z could have one more letter like Pavir.Aa00001. Digit width of N in a) is variable ranging from 1 to 3, dot (period) is optional, and Prefix is made up from organism genus and species or chosen by community. Transcript name is locus name plus . plus digits (transcript number digit), for example, Glyma.01G000100.1. Initially transcript having digit 1 is longest but in subsequent gene annotation, transcript with digit 1 can be lost or not longest any more. The longest transcript should be looked up from GFF3 file with attribute longest=1. Initially, locus/gene number is ordered and increased by 100 from chromosome left to right in a), but this is very likely to change when genome assembly and/or gene annotation is updated. Please refer to external source for naming pattern for third party gene sets in Phytozome.
+
+Files in the annotation subdirectory:
+1) Ppatens_947_v7.1.P14.annotation_info.txt.gz
+   A summary of annotation details available in Phytozome. This is a tab-delimited file, as follows:
+   (Note: Columns are blank if no corresponding data is available)
+   1: Phytozome internal transcript ID (potentially useful to connect to biomart datasets)
+   2: Phytozome gene locus name
+   3: Phytozome transcript name
+   4: Phytozome protein name (often same as transcript name, but this can vary)
+   5: PFAM
+   6: Panther
+   7: KOG
+   8: KEGG ec
+   9: KEGG Orthology
+  10: Gene Ontology terms (NOTE: these are automated results from interpro2go in most genomes, *not* empirically derived)
+  Rest of columns are for best hit (please read file header)
+
+"Best hits" are defined as the top result returned from BLASTP alignment of this species proteome to the target 
+    (A. thaliana, O. sativa, or C. reinhardtii listed above). This was run with blast+ 2.2.26 with parameters:
+    blastall -p blastp -F "mS" -b 1500 -v 1500 -e 0.001 -M BLOSUM45
+    and further filtered with an 1E-3 cutoff e-value.
+"Best hits" can also be obtained fron inparanoid computes against target(s) if not by BLASTP for newer gene set release
+
+2) Ppatens_947_v7.1.cds.fa.gz and Ppatens_947_v7.1.cds_primaryTranscriptOnly.fa.gz
+   Nucleotide FASTA format file of all gene coding sequences, with or without alternative splice variants
+
+3) Ppatens_947_v7.1.protein.fa.gz and Ppatens_947_v7.1.protein_primaryTranscriptOnly.fa.gz
+   Amino acid FASTA format file of all gene coding sequences, with or without alternative splice variants
+
+4) Ppatens_947_v7.1.transcript.fa.gz and Ppatens_947_v7.1.transcript_primaryTranscriptOnly.fa.gz
+   Nucleotide FASTA format file of spliced mRNA transcripts (UTR, exons), with or without alternative splice variants
+
+5) Ppatens_947_v7.1.gene.gff3.gz
+   GFF3 format representation of all mRNA sequences (UTR, CDS). Genomic coordinates are relative to the reference 
+   sequence in column 1
+
+6) Ppatens_947_v7.1.gene_exons.gff3.gz
+   GFF3 format representation of all mRNA sequences as above, but with exon subfeatures. Genomic coordinates are 
+   relative to the reference sequence in column 1
+
+7) Ppatens_947_v7.1.P14.defline.txt.gz
+   Tab-delimited list of all defline for the Phytozome transcript in the first column or provisional defLine (pdef type in second column).
+   Provisional deflines (aka auto defline) are generated via an automated method that prioritizes KEGG/EC over Panther over KOG 
+   over PFAM annotations, and then chooses the one with lowest multiplicity (M), where M indicates how many other genes in this genome 
+   have the same annotation.
+
+-----
+Files in the assembly subdirectory:
+1) Ppatens_947_v7.1.fa.gz
+   Nucleotide FASTA format of the current genomic assembly
+
+-----
+Files in the additional subdirectories (expression, diversity, etc.) are releases of data related to the current 
+   annotation, and are not always available for all organisms.

data/outgroup_eval_only/README.txt

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+Contains sequences from the following species and assemblies:
+Tomato: ITAG5
+Spreading Earthmoss: v7.1
+Aspergillus nidulans: ASM1142v1
+Zebra Fish: GRC12tu
+
+None of these species showed up in the training of any Pcad2 base model or in the training of the Genecad head (at time of writing June 11th, 2026).