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/obiphylo/tree.go

@@ -0,0 +1,71 @@
+package obiphylo
+
+import (
+	"fmt"
+	"math"
+	"strings"
+)
+
+type PhyloNode struct {
+	Name       string
+	Children   map[*PhyloNode]float64
+	Attributes map[string]any
+}
+
+func NewPhyloNode() *PhyloNode {
+	return &PhyloNode{}
+}
+
+func (n *PhyloNode) AddChild(child *PhyloNode, distance float64) {
+	if n.Children == nil {
+		n.Children = map[*PhyloNode]float64{}
+	}
+	n.Children[child] = distance
+}
+
+func (n *PhyloNode) SetAttribute(key string, value any) {
+	if n.Attributes == nil {
+		n.Attributes = make(map[string]any)
+	}
+	n.Attributes[key] = value
+}
+
+func (n *PhyloNode) GetDistanceToChild(child *PhyloNode) float64 {
+	return n.Children[child]
+}
+
+func (n *PhyloNode) GetAttribute(key string) any {
+	return n.Attributes[key]
+}
+
+func (n *PhyloNode) Newick(level int) string {
+	nc := len(n.Children)
+	result := strings.Builder{}
+	result.WriteString(strings.Repeat(" ", level))
+	if nc > 0 {
+		result.WriteString("(\n")
+		i := 0
+		for child, distance := range n.Children {
+			result.WriteString(child.Newick(level + 1))
+			if !math.IsNaN(distance) {
+				result.WriteString(fmt.Sprintf(":%.5f", distance))
+			}
+			i++
+			if i < nc {
+				result.WriteByte(',')
+			}
+			result.WriteString("\n")
+		}
+		result.WriteString(strings.Repeat("  ", level))
+		result.WriteByte(')')
+	}
+	if n.Name != "" {
+		result.WriteString(n.Name)
+	}
+
+	if level == 0 {
+		result.WriteString(";\n")
+	}
+
+	return result.String()
+}