Changes to be committed:

modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitaxonomy/main.go
	modified:   pkg/obiformats/csvtaxdump_read.go
	modified:   pkg/obiformats/ecopcr_read.go
	modified:   pkg/obiformats/ncbitaxdump_read.go
	modified:   pkg/obiformats/ncbitaxdump_readtar.go
	modified:   pkg/obiformats/newick_write.go
	modified:   pkg/obiformats/options.go
	modified:   pkg/obiformats/taxonomy_read.go
	modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obiiter/extract_taxonomy.go
	modified:   pkg/obioptions/options.go
	modified:   pkg/obioptions/version.go
	new file:   pkg/obiphylo/tree.go
	modified:   pkg/obiseq/biosequenceslice.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitools/obiconvert/sequence_reader.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitaxonomy/obitaxonomy.go
	modified:   pkg/obitools/obitaxonomy/options.go
	deleted:    sample/.DS_Store

pkg/obitools/obiconvert/sequence_reader.go

@@ -133,7 +133,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 		case "csv":
 			iterator, err = obiformats.ReadCSV(os.Stdin, opts...)
 		default:
-			iterator = obiformats.ReadFastSeqFromStdin(opts...)
+			iterator, err = obiformats.ReadSequencesFromStdin(opts...)
 		}
 
 		if err != nil {

pkg/obitools/obitag/obitag.go

@@ -186,6 +186,9 @@ func Identify(sequence *obiseq.BioSequence,
 				// log.Debugln("Need of indexing")
 				newidx++
 				idx = obirefidx.IndexSequence(seqidxs[i], references, &refcounts, taxa, taxo)
+				if len(idx) == 0 {
+					log.Panicf("%s idx: %v", references[seqidxs[i]].Id(), idx)
+				}
 				references[seqidxs[i]].SetOBITagRefIndex(idx)
 				log.Debugln(references[seqidxs[i]].Id(), idx)
 			}

pkg/obitools/obitaxonomy/obitaxonomy.go

@@ -91,6 +91,7 @@ func CLINewickWriter(iterator *obitax.ITaxon,
 		obiformats.OptionsWithRank(CLIWithRank()),
 		obiformats.OptionsWithScientificName(CLIWithScientificName()),
 		obiformats.OptionsWithTaxid(true),
+		obiformats.OptionWithoutRootPath(CLINewickWithoutRoot()),
 	)
 
 	filename := obiconvert.CLIOutPutFileName()

pkg/obitools/obitaxonomy/options.go

@@ -25,6 +25,8 @@ var __to_dump__ = ""
 var __download_ncbi__ = false
 var __extract_taxonomy__ = false
 var __newick__ = false
+var __newick_with_leaves__ = false
+var __newick_without_root__ = false
 
 func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__rank_list__, "rank-list", false,
@@ -81,6 +83,9 @@ func OptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__newick__, "newick-output", __newick__,
 		options.Description("Format the resulting taxonomy as a newick tree"),
 	)
+	options.BoolVar(&__newick_without_root__, "without-root", __newick_without_root__,
+		options.Description("If used, do not include the non-branched path to the root in the output"),
+	)
 
 }
 
@@ -166,6 +171,14 @@ func CLIAsNewick() bool {
 	return __newick__
 }
 
+func CLINewickWithLeaves() bool {
+	return __newick_with_leaves__
+}
+
+func CLINewickWithoutRoot() bool {
+	return __newick_without_root__
+}
+
 func CLIAskForRankList() bool {
 	return __rank_list__
 }